A French Atlantic 2 maritime patrol aircraft and a German P-3C Orion were conducting regular flights as part of a Nato exercise and behaved in accordance with international law, the two countries said.
Russia's Su-27 jet returned to base after the French and German planes turned away from Russia, the ministry said.
It said it had scrambled the jet to "prevent the Russian state border being violated".
"Our P-3C Orion was on a surveillance mission over the Baltic Sea and flying, as per standard, towards Kaliningrad," a spokesman for the German Navy said.
"There was never any intention to enter Russian airspace. These aircraft always keep a safe distance. These flights are routine, and we don't do anything to cause a provocation."
Kaliningrad is a Russian exclave wedged between Poland and Lithuania on the Baltic sea,
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France's Armed Forces Ministry also confirmed the incident.
"As part of a Natp exercise, a Russian Su-27 fighter jet interacted with an Atlantic 2 maritime patrol aircraft off the Baltic States today," the ministry said.
"The approach was conducted in international airspace over the Baltic Sea and was professional and controlled.: