Coast guard vessels stopped the ship two nautical miles from Perama -- a coastal industrial district west of Athens proper -- and forced it return to port.
The American skipper of the ship was sent before a Piraeus prosecutor hours after his arrest -- a flangrante delicto process -- who slapped him with felony charges. The defendant requested and received a 48-hour stay to provide a statement. He remained in custody.
The ship is part of a nine-vessel flotilla, carrying activists and aid to Gaza, which aims to breach the Israeli navy's sea blockade of the Palestinian enclave.
On Friday, Citizens Protection Minister Christos Papoutsis announced that vessels registered under the Greek or a foreign flag are banned from leaving Greek ports if destined for the sea region of Gaza, a decision that drew sharp criticism by the flotilla's activists and supporters.