Aida Cruises said it plans to drop all calls in Israel for the next two months, because of security concerns.
"The well-being and safety of our guests has absolute priority," Hansjorg Kunze, the German line's vice president for communication and sustainability, said in a statement.
The decision follows a July 7 departure of the AidaDiva from Ashdod, near Tel Aviv, in which explosions could be seen from the ship.
Debris fell on the open deck that "may have come from defense missiles," the statement said.
Militants have stepped up rocket attacks on Israel in recent days after the suspected murder of a Palestinian teenager.
Aida said there were no injuries, no damage to the ship and all 2,700 passengers and crew were "doing well." It said the ship left without interruption and is expected in Crete at 8 a.m. July 9.
On remaining July and August itineraries, the Greek island of Santorini will be substituted for scheduled port calls in Ashdod, the statement said.
All guests of Aida Cruises who have booked one of the cruises in question will be informed immediately, the statement said. Follow @tstravelweekly on Twitter.