Russia's Defence Ministry said the Il-20 reconnaissance aircraft, with 15 Russian service personnel on board, was brought down by anti-aircraft batteries of Moscow's ally, Syria, in a "friendly fire" incident.
"This absolutely does not correspond to the spirit of Russian-Israeli partnership", Russian Defence Ministry spokesman Igor Konashenkov told Russian state media, Reuters noted.
The defense ministry in Moscow said the aircraft was returning to the Russian-run Hmeymim airbase when, at about 11:00 p.m. Moscow time on September 17, it lost radar contact.
It added that by the time the Russian plane was struck, the Israeli jets were already out of Syria and back in their own airspace.
Speaking alongside Russian President Vladimir Putin at talks in Sochi on Monday, Turkey's President Recep Tayyip Erdogan said the creation of a 15-20 kilometer (approximately 9-12 miles) demilitarized zone will prevent a "humanitarian crisis" in the northwestern province.
Putin has stated that the downing "looks like a chain of tragic circumstances because the Israeli plane didn't shoot down our jet". "And these will be steps that everyone will notice", he said.
The demilitarised zone will be secured with the help of "mobile patrol groups of Turkish contingents and contingents of Russian military police", Putin said.
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Syrian state media claimed the country's military had shot down a number of incoming missiles.
Israel is widely believed to have been behind a series of air strikes mainly targeting Iranian and Hezbollah forces in Syria that have joined the country's war fighting alongside the government.
Earlier, the Russian defence ministry had said that the plane had gone off the radar around 11pm during an attack by four Israeli F-16 jets over Syrian infrastructure in the province of Latakia, a stronghold of President Bashar al-Assad.
The Israeli government is concerned by what it calls Iran's "military entrenchment" in Syria, as well as shipments of Iranian weapons to the Hezbollah. However, officials in Moscow are blaming Israel for the incident. Fifteen Russian servicemen were killed during the incident, but officials in Moscow and Tel Aviv moved quickly to defuse tensions even though the Russian Ministry of Defense initially responded with fury against the Israelis.
When two or three allies coordinate forces, as Russian Federation has with Syria and Iran, they use communications protocols to identify friendly aircraft in the air.
Moscow says the trace of the Il-20 on flight control radars disappeared during an attack by four Israeli F-16 jets in Latakia.
The Israeli and Russian militaries maintain what they call a "deconfliction mechanism", which is meant to coordinate their activities in Syria in order to avoid incidents like this one.
Israel says that it did warn Moscow of its impending raid on Syria via its deconfliction line.