The Greek State established the Ministry of the Aegean in 1985 by the unanimous vote of the Greek Parliament. Ιn 2004 the Ministry of the Aegean was renamed to Ministry of the Aegean and Island Policy. In 2009 the Ministry of the Aegean and Island Policy was affiliated with the Ministry of Infrastructure Transport and Networks. From September 2010 the Secretariat General is affiliated with the Ministry of Maritime Affairs Islands and Fisheries.

Its establishment and operation illustrates the importance of the government to implement specific strategies of parity convergence and harmonization to the mainland area aiming at the development of the Aegean.