Israel's ambassador to France has been summoned to the country's foreign ministry and warned about Israeli flights over UN positions in Lebanon.
Israeli jets have been involved in several incidents over Lebanon
Earlier, the French defence minister said troops serving in Lebanon had been seconds from firing on Israel's jets.
Michele Alliot-Marie told parliament the jets dived towards UN positions in October and were perceived as a threat.
Israel's ambassador, Daniel Shek, said the flights were "not aggressive" and may have been misinterpreted.
French Foreign Minister Philippe Douste-Blazy said he had told Israel that it must stop such acts.
"I believe he understood perfectly. We concluded that this must not happen again," Mr Douste-Blazy told French radio station, France Inter.
Mr Douste-Blazy told the radio station that the jets had appeared to be carrying out practice bombing runs.
But after the meeting, the Israeli ambassador said the French troops had misunderstood the manoeuvres of the jets.
"All the Israeli air force's flights over Lebanon have one sole purpose, they are reconnaissance flights. There is no exception to the rule," Mr Shek told the news agency AFP.
French troops are in Lebanon as part of the UN peacekeeping mission, which was expanded in a UN-brokered deal that ended a 34-day conflict between Israel and Hezbollah militants earlier this year.
France has previously complained about Israel violating Lebanese air space.
The head of France's troops in Lebanon even suggested their rules of engagement might need to be changed so that they could reply with force to Israel's air violations.
Ms Alliot-Marie that a "catastrophe" was avoided in the October incident only thanks "to the judiciousness of our troops".
Israeli warplanes have been involved in a number of recent incidents in the region.
Eight jets staged mock raids on Hezbollah targets in Beirut, flying low and diving, at the end of October, according Lebanese security forces.
Reports from Germany alleged that Israeli planes buzzed a German warship off the Lebanese coast, and fired shots nearby. Israel said the jets were merely investigating an unreported take-off.
Israel has previously warned that it would continue to fly over Lebanon to prevent Hezbollah from rearming with weapons smuggled from Syria.