A report in the Der Tagesspiegel newspaper quoted a German junior defence minister as telling a parliamentary committee that two Israeli F-16 fighters flew low over the ship, firing twice.
The jets also activated infrared countermeasures to ward off any rocket attack, the paper said, in an advance release ahead of Thursday's edition.
The minister did not say when the incident happened or what had caused it.
"I can confirm that there was an incident," a ministry spokesman said on Wednesday. He declined to give further details as an investigation was under way.
An Israeli military spokeswoman denied that the incident had taken place.
She said the German statements appeared to refer to an incident that took place on Tuesday.
Jets were scrambled when a helicopter took off from a German aircraft carrier close to Israeli waters without identifying itself.
The pilots of the planes realised the mistake, did not engage the helicopter and returned home, the spokeswoman said.
UN naval force
Germany assumed command of a United Nations naval force off Lebanon 10 days ago, and has sent eight ships and 1,000 service personnel to join the international peace operation in the region.
The naval force is charged with preventing weapons-smuggling and helping maintain a ceasefire between Israel and Hezbollah.
The Israeli air force has come under heavy criticism for continuing flights over southern Lebanon since a 34-day war between Israel and Hezbollah ended on August 14 with a UN-sponsored truce and the expansion of the United Nations peacekeeping force.
Amir Peretz, Israel's defence minister, said at the weekend that the flights would continue because of alleged arms smuggling to Hezbollah.
The Lebanese government and the UN say the overflights, which Israel had conducted since ending its 22-year occupation of south Lebanon in 2000, violate both the latest truce and the terms of Israel's earlier pullout.