The incident, which Israel has so far denied, was one of two involving the Israeli military and German forces in the region this week, defence spokesman Thomas Raabe told reporters.
"There have been two incidents, one involving a helicopter and another the Alster" a German electronic surveillance and reconnaissance ship.
Raabe said six Israeli F-16 fighter planes had fired shots into the air over the Alster on Tuesday while the ship was in international waters some 50 nautical miles off the Israeli coast.
The confrontation came just days after Germany assumed command of the marine component of the UN peacekeeping forces in Lebanon (UNIFIL) on October 18, in its first military foray into the Middle East since World War II.
Raabe said in a separate incident, Israel claimed that a German helicopter in the region had failed to identify itself.
Defence Minister Franz Josef Jung and his Israeli counterpart Amir Peretz have discussed the events, he said.
"It has been dealt with. In future we expect smooth co-operation with the Israeli forces," he said.
The Alster has been deployed in the Mediterranean to back up German vessels patrolling the Lebanese coast in a bid to prevent arms being smuggled to Hizbullah by sea, Raabe said.
Israel was informed of the presence of the ship and should have known that it was unarmed and therefore not a threat, he said.
"The Israeli military is highly skilled and I believe Israel can and should tell the difference between a frigate and a reconnaissance ship."
He added however: "We must also understand that Israel faces great security challenges."
Israel has been reprimanded by the United Nations for carrying out military flights over Lebanon since the end of its 34-day war on its northern neighbour to rout Hizbullah militia.
But Peretz has said the flights would continue because arms were still flowing towards Hizbullah.

Copyright AFP (Agence France-Presse), 2006