Gentvilas confirmed his decision at a news conference on Wednesday.
Transport Minister Eligijus Masiulis has told BNS on Tuesday that one of the port's senior officials will temporarily take on the duties of the CEO, with a competition for a new CEO to be launched after the new government takes office.
Gentvilas, who has been the port's CEO since June 2009, is number three on the Liberal Movement's list after the recent general election, in which the party won a total of ten parliamentary seats.