The defence ministry said Israeli jets put the Il-20 plane into the path of Syrian air defence systems on Monday after failing to give Moscow enough warning of a strike on Syrian targets.
The Il-20 disappeared off the radar at about 23:00 local time (20:00 GMT).
Israel is yet to comment on the allegations.
It rarely acknowledges carrying out strikes on Syria, but an Israeli military official recently said it had hit more than 200 Iranian targets in Syria over the past 18 months.
The Israeli government is concerned by what it calls Iran's "military entrenchment" in Syria, as well as shipments of Iranian weapons to the Lebanese militant group Hezbollah, which is fighting alongside Syrian government forces.
What exactly happened?
The details are murky, and Russia's account of the incident has yet to be verified.
According to reports, Monday's incident occurred about 35km (22 miles) from the Syrian coast as the Ilyushin Il-20 aircraft was returning to Russia's Hmeimim airbase near the north-western city of Latakia.
Russia's Tass news agency says the Il-20 plane "disappeared during an attack by four Israeli F-16 jets on Syrian facilities in Latakia province".
Reports on Syrian state media spoke of an attack in the area shortly before the plane disappeared. According to Sana news agency, the military said it had intercepted "enemy missiles coming from the open sea towards the city of Latakia".
Syrian television also reported explosions over the sky in Latakia just before 22:00. Thirty minutes later, the Sana Facebook page reported that Syrian air defences had responded to enemy missiles.
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