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Here is the information about fairway dues in the Maritime Safety Act (unofficial translation into English available on the Riigi Teataja website):

Chapter 111 FAIRWAY DUES
[RT I, 31.12.2012, 1 - entry into force 01.07.2013]
§ 501. Fairway dues

(1) Fairway dues are dues for navigational organisation, and the use of icebreaking and information services on public waterways, as well as for the use of the infrastructure installed on public waterways to ensure maritime safety.

(2) Fairway dues shall be paid upon arrival of a ship at an Estonian port or a roadstead of an Estonian port. Fairway dues shall be paid for all ships irrespective of their flag state.

(3) Fairway dues shall be paid by the operator or the ship’s agent.

(4) Fairway dues shall be paid into the state budget. The Maritime Administration shall calculate fairway dues and issue corresponding payment notices.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
§ 502. Payer of dues

[Repealed - RT I, 31.12.2012, 1 – entry into force 01.07.2013]
§ 503. Receipt of dues

[Repealed - RT I, 31.12.2012, 1 – entry into force 01.07.2013]
§ 504. Calculation of fairway dues

[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(1) The Maritime Administration shall calculate fairway dues upon arrival of a ship at a port or a roadstead of a port once every twenty-four hours if at the roadstead of the port the ship is loaded, unloaded, supplied with provisions (food, water etc.), repaired, or the ship is associated with commercial activities in any other similar manner.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(11) If, after arrival at a port or roadstead of a port a ship leaves for another port or a roadstead of another port in the same region of ports, fairway dues shall be calculated for one arrival. The regions of ports are the following:
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
1) the eastern part of the Gulf of Finland, including the ports east of the meridian 25°30'E;
[RT I, 22.12.2010, 1 – entry into force 02.01.2011]
2) the western part of the Gulf of Finland, including the ports between the meridians 24°00'E and 25°30'E;
[RT I, 22.12.2010, 1 – entry into force 02.01.2011]
3) Western Estonia, including the ports west of the meridian 24°00'E, excluding the ports specified in clause 4) of this subsection;
[RT I, 22.12.2010, 1 – entry into force 02.01.2011]
4) the Gulf of Riga, including the ports east of the meridian 23°55'E and the ports on the island of Ruhnu.
[RT I, 22.12.2010, 1 – entry into force 02.01.2011]

(12) If, within a period of twenty-four hours, a ship enters several ports or roadsteads of several ports within different regions of ports, the Maritime Administration shall calculate fairway dues for one arrival.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(13) [Repealed - RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(2) The Maritime Administration shall submit to the operator or the ship’s agent a payment notice concerning the fairway dues subject to payment, prepared on the basis of the ship’s general declaration or the pilot bill. A payment notice for a calendar month regarding a ship providing a regular service shall be submitted by the fifth day of the following month, and a payment notice regarding other ships shall be submitted within 30 days after the date of arrival of the ship at a port or roadstead of a port.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(21) A payment notice regarding a ship providing a regular service and entering an Estonian port five or more times per month shall be prepared for no more than five entries per month. Payment notices for more than five entries shall be prepared during the following months, but for no more than five entries per month. For the last month in a calendar year, the payment notice concerning the fairway dues shall be prepared for all entries subject to payment.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(22) If a ship providing a regular service is replaced with another ship, the total number of entries made by such ships shall be calculated for the purpose of reducing the fairway due, and first of all, the entries made in the course of the regular service provided during a calendar year by the ship with a higher fairway due rate shall be taken into account as the times payable for under in subsection 5010 (1) of this Act. If the ship with the higher fairway due rate has entered a port less times than the number provided for in subsection 5010 (1) of this Act, the fairway due payable for the remaining times shall be calculated according to the rate applicable to the ship with the second highest fairway due rate. If a payment notice has been prepared for a ship with the smaller fairway due rate before the replacement of the ship, but the fairway due with the higher rate is payable for the full calendar year, a setoff of fairway dues shall be made not later than in the last month of the calendar year, and a fairway due shall be added to the payment notice in the amount by which the fairway due was previously calculated less. This subsection is applied to the ships of one and the same operator.
[RT I, 29.06.2014, 110 – entry into force 09.07.2014]

(23) If according to the timetable referred to in subsection 5010 (12) of this Act, fairway dues shall be paid at a lower rate than for 60 times during a calendar year pursuant to clause 5010 (1) 1) of this Act, the Maritime Administration shall prepare payment notices pursuant to the procedure provided in the first sentence of subsection 504 (21) until the maximum number of entries made by the respective ship and payable for during a calendar year is achieved. If the timetable is changed during a calendar year, and therefore the fairway dues payable for the passenger ship during the calendar year pursuant to clause 5010 (1) 1) change, a setoff of fairway dues shall be made not later than in the last month of the calendar year, and a fairway due shall be added to the payment notice in the amount by which the fairway dues were previously calculated less, or the overpaid amount shall be returned.
[RT I, 30.12.2014, 3 – entry into force 01.01.2015]

(3) A payment notice shall set out:
1) the given name, surname and position of the official preparing the payment notice;
2) the date of preparation of the payment notice;
3) the name and address of the payer;
4) the amount of fairway dues subject to payment;
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
5) the legal and factual basis for the notice, including the bases for the calculation of the amount of the fairway dues, reduction or increase of the due rate;
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
6) the due date for payment;
7) a warning concerning the obligation to pay a fine for delay and the commencement of compulsory enforcement in case of failure to pay fairway dues by the due date.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(4) The term for payment of fairway dues is 30 days after the date of receipt of a payment notice, unless otherwise provided for in this Act.
[RT I, 30.12.2014, 3 – entry into force 01.01.2015]

(5) Fairway dues for ships providing a regular service shall be paid by the 25th day of the following month.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
§ 505. Rates of fairway dues

(1) Fairway dues shall be calculated on the basis of a ship’s gross tonnage (GT) which is multiplied by the unit price.

(2) The unit price for a cruise ship is 0.12 euro.

(3) The unit price for other types of ship is the following, on the basis of ice class:
1) 1A Super or an equivalent ice class – 0.28 euro;
2) 1A or an equivalent ice class – 0.30 euro;
3) other ice class or no ice class – 0.35 euro.

(4) The maximum amount of fairway dues per one voyage is 20,000 euros for a tanker, 12,000 euros for a cruise ship and 15,000 euros for other types of ships.
[RT I, 31.12.2012, 1 – entry into force 01.01.2014]
§ 506. Payment of fairway dues

[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(1) An operator or a ship’s agent is required to transfer the fairway dues to the bank account specified in the payment notice by the due date indicated in the payment notice.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(2) The Maritime Administration shall submit a statement of holdings concerning receipt of dues to the operator or ship’s agent at his or her request.
[RT I 2005, 31, 229 – entry into force 03.06.2005]
§ 507. Fine for delay and compulsory enforcement

[RT I 2008, 47, 263 – entry into force 16.11.2008]

(1) If an operator or a ship’s agent has not paid fairway dues by the due date, the operator or ship’s agent is required to pay a fine for delay at the rate of 0.05 per cent per day on the overdue amount, but the total amount shall not exceed the fairway dues indicated in the payment notice submitted to the operator or ship’s agent by the Maritime Administration.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(2) A payment notice on which the payment of fairway dues is based is an administrative act for the performance of a financial obligation in public law within the meaning of clause 2 (1) 21) of the Code of Enforcement Procedure. If an operator or ship’s agent fails to pay fairway dues by the due date, the Maritime Administration has the right to submit the payment notice for compulsory enforcement within seven years after the due date of payment.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
§ 508. Obligation of port authority

[RT I 2009, 37, 251 – entry into force 10.07.2009]

(1) A port authority is required to present to the Maritime Administration the timetables of ships providing a regular service according to timetables.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]

(2) The timetable for the coming calendar month shall be presented not later than on the last working day of the current month.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
§ 509. Exemptions

(1) The following are exempted from payment of fairway dues:
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
1) ships performing administrative duties and owned by the Republic of Estonia;
2) military vessels of the Republic of Estonia;
3) floating hospitals, training vessels and ships engaged in research in Estonia;
4) ships participating in international non-commercial cooperation programmes in which Estonia is involved;
5) foreign ships which arrive for a state visit;
6) ships which arrive in order to transport sick persons, survivors of a marine casualty or the deceased;
7) fishing vessels;
8) ships providing a connection between the Estonian mainland and the islands, including mail ships;
9) ships bunkering at a roadstead and ships delivering bilge water, tank washing water and waste oil if they do not enter Estonian ports;
10) ships which stay only at a roadstead to find refuge from storm.

(2) [Repealed - RT I, 31.12.2012, 1 – entry into force 01.07.2013]
§ 5010. Reduction of due rates

(1) Fairway dues shall be paid during a calendar year for a maximum of:
1) 60 times by a passenger ship, whereas for a half of the number of entries made by a passenger ship providing a regular service, but not for over 60 times;
[RT I, 30.12.2014, 3 – entry into force 01.01.2015]
2) 3 times by a cruise ship;
3) 10 times by other types of ship.

(11) In order to apply the specification provided for in subsection 504 (22) of this Act upon replacement of a ship providing a regular service with another ship, the operator shall immediately inform the Maritime Administration about the necessity for replacement of the ship providing a regular service.
[RT I, 29.06.2014, 110 – entry into force 09.07.2014]

(12) If fairway dues shall be paid for less than 60 times during a calendar year for a passenger ship providing a regular service pursuant to clause (1) 1) of this section, the operator of the passenger ship or the ship’s agent shall submit a timetable for the voyages planned for the given calendar year to the Maritime Administration not later than by the end of the calendar month preceding the voyages undertaken pursuant to the timetable. If the timetable is changed during the calendar year, the operator or the ship’s agent shall immediately inform the Maritime Administration about the respective changes.
[RT I, 30.12.2014, 3 – entry into force 01.01.2015]

(2) 30 per cent of the rate of the fairway dues shall be paid for a ship on a roadstead if the ship does not enter a port.

(3) If a port is not serviced by icebreakers on the basis of § 50 (1) of this Act, an operator or ship’s agent shall pay 70 per cent of the rate of the fairway dues provided for in § 505 of this Act.

(4) 50 per cent of the rate of the fairway dues shall be paid for a ship that has arrived to undergo repairs in case the ship is not loaded or unloaded and does not take on board or let go ashore passengers.

(5) The fairway dues for double hull oil tankers with segregated ballast tanks shall be calculated on the basis of the reduced gross tonnage of the ship which is set out in the tonnage certificate issued pursuant to the International Convention on Tonnage Measurement of Ships of 1969. The reduced gross tonnage shall be taken into account if a corresponding notation is entered in the section “Notations” of the tonnage certificate of the ship.
[RT I, 31.12.2012, 1 – entry into force 01.07.2013]
§ 5011. [Repealed - RT I, 22.12.2010, 1 – entry into force 02.01.2011]