According to the ministry, the plane conducted on Monday a coordinated transfer flight to an airfield in Russia's exclave of Kaliningrad in the Baltic region while flying with a switched-on transponder.
"During the flight, the crew of the plane was in contact with Estonian air traffic controllers, who did not make any complaints against the actions of the crew," the ministry said in a statement.
"The flight was carried out in strict accordance with the international rules for the use of airspace without violating the borders of other states, which has been confirmed by means of objective monitoring," the statement said.
Earlier, the Estonian Defense Forces stated that a Russian-owned Il-76 aircraft entered the airspace of Estonia at around 1 pm Moscow time around the island of Vaindloo. The Estonian Foreign Ministry summoned the Russian ambassador in Tallinn and handed him a note.