The plane was detected at about 2:30 p.m. GMT Thursday after it had crossed five kilometers (3 miles) into Russian territory from the Baltic state.
"Estonia's Defense Forces have no involvement in the violation of Russia's airspace," a General Staff news release said. "The plane was a civilian one. As is known, there are no aircraft on service in the Estonian Defense Forces."
An aide to the commander of the Russian Air Force, Alexander Drobyshevsky, said earlier on Friday that the trespasser was a lightweight trainer plane and that it had been flying at an altitude of over 10,000 meters (32,000 feet) and at a speed of 800 km/hr (500 miles/hr).