"The Russian plane did not violate the state borders of Estonia. On June 22, 2015 the An-26 transport plane was conducting a planned flight from the Kaliningrad region to St. Petersburg," the ministry said in a statement.
"The flight was carried out over the neutral waters," the statement said.
Russia's long-range aviation has been increasing the number and duration of planned flights in recent years, causing NATO to voice concern over alleged violations of the airspace of member states. The accusations have become more frequent as relations between NATO and Moscow soured over the Ukrainian crisis.
Meanwhile, the military alliance has been building up its presence in Eastern Europe, sending tanks and paratroopers to hold military drills along Russia's western borders.