In 1947 in the waters of the Nagayevo Bay laden with explosives blew up the ship "General Vatutin".

[2] Technique, cargo, port facilities, commercial and administrative buildings - all were destroyed from that blast.

A Decree of the Council of Ministers of the Russian Federation signed on 30.08.1993 No.1551-p ordered the opening of the port for international maritime freight and passenger traffic.

In July 2009, government resolution No.926[3] signed by Prime Minister Vladimir Putin established the boundaries of Magadan port, the port declared a register of Russian seaports.

With decree N1288 of 22/06/2016 of the Russian Federation Government, the Port of Magadan was added to a list of Russian seaports accepting ships carrying nuclear materials and radioactive substances.