The Ministry for Naval Affairs was established during the early years of the modern Greek state, reflecting the country's long-standing maritime traditions and the importance of shipping and seafaring to its economy and society.

Greece's strategic geographic position and its numerous islands made the maritime sector a key element of national life and policy.

[1][2] After the reorganization of the government under Ioannis Kapodistrias, and in the early years of King Otto's rule, it was known as the Secretariat of State for Naval Affairs (Γραμματεία τῆς Ἐπικρατείας ἐπὶ τῶν Ναυτικῶν), but after 1843 it was renamed to its eventual name (Ὑπουργείον ἐπὶ τῶν Ναυτικῶν, later simplified Ὑπουργείον τῶν Ναυτικῶν).

In 1950, the Nikolaos Plastiras government established the Ministry of National Defence, to which the Ministry for Naval Affairs was subordinated as a Sub-Ministry (Ὑφυπουργείον τῶν Ναυτικῶν) until 1953, when the Alexandros Papagos government abolished the position.

The Ministry for Naval Affairs was responsible for a range of issues related to Greece's maritime and shipping industries.