Russia had tried to "take control" of French air force and navy patrols, he told the broadcaster RTL, adding that Russia was "pushing the limits" with such behaviour.
"A Russian air traffic system threatened to shoot down French planes over the Black Sea" that were patrolling in international airspace at the time, Lecornu said.
"You have Russian operators threatening French pilots with the shooting down of their aircraft," he said.
The incident took place a "month ago" but his ministry later said it had actually happened in November and involved a French AWACS aircraft specialising in airborne control and detection operations.
"It was a particularly aggressive radio exchange," a ministry spokesperson said, calling such an intimidation attempt in that particular area was "a first".
In a separate incident, a Russian warship was detected near the Bay of the Seine, an inlet of the English Channel on France's Normandy coast, Lecornu said.
Although the Russian vessel was in international waters, "it was as if it had come to intimidate France", he said.
His remarks are the latest in a string of French accusations of aggressive Russian behaviour, including alleged cyberattacks and propaganda directed at France.
Such incidents were "as old as the Cold War", Lecornu acknowledged, but warned that "Russia is pushing the limits in terms of aggressive behaviour".
One cyberattack had targeted a French weapons factory, he said.
Lecornu last weekend ordered his ministry to be more vigilant towards Russian "sabotage and cyberattacks", according to an internal directive seen by AFP on Tuesday.
President Emmanuel Macron's government is a major supplier of weapons and aid to Ukraine, which has been fighting Russia's invasion for the past two years.
Macron declared last month that Europe's priority must be to "not let Russia win".
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