It was mainly tasked with implementing national economic policies and maritime safety in Estonian territorial and navigable inland waters.

On 13 November 1918, after the departure of German occupation forces, the Estonian Provisional Government took over the Maritime Safety and Navigational Auxiliary Service and then formed the agency as part of the Command of Tallinn Port.

[2] The decision to establish the Estonian Maritime Administration was made on December 1, 1989, and the agency was formed on 16 January 1990.

The first statute of the Estonian Maritime Administration was approved on 29 April 1990, and the agency was tasked with preparing the Merchant Shipping Code, which was accepted on December 9, 1990.

In the beginning, the main tasks of the organization included icebreaking, offering piloting services and fulfilling coast guard duties, like maritime rescue and oil pollution control.