It said Syrian forces mistakenly downed the Il-20 reconnaissance plane with an S-200 air-defense missile as they attempted to fight off an attack by Israeli planes.
The Russian Defence Ministry said a recovery operation in the Mediterranean Sea is underway and that it has already located the wreckage in the sea and has retrieved some bodies and some fragments of the plane.
Around the time the plane disappeared, regime media reported that the Syrian coastal city of Latakia - near a Russian airbase the Il-20 was returning to - came under attack from "enemy missiles", to which regime missile defence batteries responded.
Russian defense minister Sergei Shoigu said he had spoken with Israeli defense minister Avigdor Lieberman, according to TASS, and told his counterpart that "such actions will not be left unanswered by us".
Russian Federation initially blamed "irresponsible" Israeli actions, but President Vladimir Putin said on Tuesday it was "a chain of tragic accidental circumstances".
Putin told Tuesday's press conference, however, that any steps taken by Russian Federation would center on ensuring the safety of its troops.
Some remains of the crew members and plane debris have been picked up by the Russian navy, the ministry said.
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.
United States and Israeli officials have said Iran and Hezbollah should end their armed presence in Syria.
Israel's military has declined to comment.
French frigate Auvergne was not involved in the disappearance of a Russian Il-20 electronic reconnaissance aircraft over Syria, a spokesman for the French military said on 18 September.
Though Syria claimed it downed numerous missiles fired by the U.S. last year and earlier this year as punishment for chemical attacks blamed on the Syrian military, it never provided any evidence.
Officials did not immediately say if the plane was shot down.
"This is absolutely not in keeping with the spirit of the Russian-Israeli partnership. Nevertheless, they deliberately carried out this provocation", Konashenkov said. In some cases, those countries are backing opposing sides in the Syrian conflict.
Moscow said its plane disappeared from radar screens as it was coming in to land at the Hmeymim air base in western Syria late on Monday, just as Israeli jets and French naval vessels were mounting air strikes on targets in the same area of Syria.
However, diplomats and military experts have warned that the risk of inadvertent strikes is high.