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 stated categorically earlier Friday that a plane caught violating Russian airspace on Thursday was not a military aircraft.
The agency said a Lear Jet 60 was on a training flight and that the private company that owned it had not asked for permission to fly in a border area because it had no intention of flying toward the frontier, but had veered off course due to pilot error.
Estonia's General Staff said earlier Friday the plane was a civilian one.
"As is known, there are no aircraft in service with the Estonian Defense Forces," it said.
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).
Chilly relations between Russia and its three former Soviet stable mates on the Baltic have been further complicated in recent years by a series of accusations of airspace violations. In September 2005, a Russian Su-27 Flanker fighter-bomber crashed in Lithuania after a malfunction caused it to veer off course. Moscow paid 19,500 euros (about $25,000) in compensation.