Pamboukis, who is not a Parliament MP and who previously served as minister of state with a portfolio that included the attraction of major international investments in the country, was reportedly criticised by other Cabinet members this week for the latter's stated support for the re-establishment of the ministry.
Pamboukis also advocated that the coast guard be returned under the jurisdiction of a re-established merchant marine ministry.
"For two months I have engaged in efforts to revitalise a nationally beneficial sector (shipping). However, these efforts have not had the desired result..." his resignation letter read.
"Recently I publicly detailed, with clarity and outspokenness, a proposal for the re-establishment of the ministry, which serves the obvious. This position, more so, has been adopted by all of the social partners and the entire shipping sector," he added.
At least two opposition parties commented Pamboukis' reaction.
Main opposition New Democracy party spokesman Yiannis Mihelakis termed it a "self-evident act of dignity," adding that "Mr. Pamboukis realised it even at a late stage and submitted his resignation."
Popular Orthodox Rally (LA.O.S) party spokesman Costas Aivaliotis said that "an intelligent and consistent minister left the government, one who preferred his dignity from the attempt at ridiculing that the deep PASOK attempted."