Ibrahim Karaosmanoglu, mayor for Izmit, said the man had claimed that there were four other hijackers on board the Kartepe ferry, travelling in the Gulf of Izmit, about 60 miles east of Istanbul.
But he said crew had told him the hijacker was alone.
There was no information on his identify or his motive but local reports said he had claimed to be a member of the outlawed Kurdistan Workers’ Party, a militant separatist movement which is regarded as a terrorist organisation by the a number of countries, including the UK.
Mr Karaosmanoglu said the man was demanding to speak to the media.
State television said coast guard boats were shadowing the ferry as it was sailing off the coast of the town of Yalova in the Sea of Marmara, which connects the Black Sea to the Aegean.
There were some 20 passengers and four crew on board.