Russian President Vladimir Putin chairs a meeting via teleconference on the situation of coal mining enterprises in Kuzbass, at the Kremlin in Moscow. AP
The alleged spy plane "descended rapidly" across the planned route for a Tel Aviv-Moscow Aeroflot service with 142 people on board, Russia's Federal Air Transport Agency said late Saturday according to news agency Interfax.
"The direction and altitude of the commercial flight were immediately altered" to avoid a collision, the agency said, adding that the unknown plane did not respond to radio hails from air traffic control.
Interfax reported that the Aeroflot flight had to drop 500 metres (1,600 feet) to keep its distance from the reconnaissance aircraft, which the pilots saw from the cockpit with the naked eye.
A second plane, a private jet flying from the Black Sea resort Sochi to Northern Macedonian capital Skopje, also had to divert to avoid the spy plane, the air transport authority said.
"Increased activity by NATO aircraft near Russia's borders... creates a risk of dangerous accidents involving civilian aircraft," the agency said, adding that it would lodge a diplomatic protest.
Russian authorities did not say which nation had operated the spy plane.
On Friday, Russian fighter jets were sent to escort two American spy aircraft over the Black Sea region, Russian media reported.
Saturday's incident comes as tensions rise between Russia and Western nations, which accuse Moscow of massing troops on its border with Ukraine in preparation for an invasion.
Russia has denied it has any such plans, in turn accusing NATO countries of "provocations" including military exercises near its borders.