"Connection has been lost with the crew of a Russian Il-20 plane over the Mediterranean Sea 35 kilometres from the Syrian coast as it was returning to the Hmeimim airbase", the Russian defence ministry said early Tuesday.
Syria is yet to make a statement on whether it was responsible for the disappearance of the Russian aircraft.
Other attacks were reported on September 4 that targeted sites in the coastal Tartus area and in Hama province.
A United States official said Washington believed the aircraft, which is an Il-20 turbo-prop plane used for electronic reconnaissance, was inadvertently shot down by anti-aircraft artillery operated by Moscow's ally, the Syrian government.
Missiles had been fired from the sea at several locations in the Syrian coastal city of Latakia on Monday but were intercepted by air defences, Syrian state media had said, before the downing of the plan was reported.
Loud explosions shook Syria's coastal province of Latakia late on Monday, sending orange flames into the sky in what Syrian state media said was an Israeli attack targeting a state company for technical industries.
According to the statement radars also recorded the launch of missiles from a French frigate stationed in the Mediterranean. Local sources say the target was an Organization for Technical Industries - a subdivision of the Syrian Ministry of Defense, linked to missile and chemical weapons development.
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The strikes followed a similar attack on Damascus International Airport late Saturday, which Syrian state media also blamed on Israel.
During the more than seven-year conflict in neighbouring Syria, Israel has grown deeply alarmed by the expanding clout of Iran, a Syrian government ally.
USA and Israeli officials have said that Iran and Hezbollah should end their armed presence in Syria.
It is unclear whether the Israeli military notified Russian Federation ahead of Monday night's attack in Latakia.
Footage shared by Syrian state TV claims to show Syrian forces firing missiles from Lattakia.
The Israeli military refused to comment on claims they were behind the attack on Syria.