Moscow's defense ministry earlier said Israeli strikes had endangered two passenger planes.
"We are very concerned by the attacks and how they were made. This is a gross violation of the sovereignty of Syria," the Russian ministry of foreign affairs said in a statement.
"The provocative actions of the Israeli air force.. directly threatened two airliners," ministry spokesman Igor Konashenkov said in a statement.
He said the attack came from over Lebanese territory and came as "two airliners, not from Russia, were preparing to land at the airports of Beirut and Damascus."
He said restrictions were imposed on the use of Syrian government forces' air defense systems "to prevent a tragedy." One of the planes was redirected to a Russian airbase within Syria.
The Russian defense ministry said three Syrian military personnel were injured in a strike that saw Israeli warplanes drop 16 bombs. Of these, 14 were destroyed by Syrian defense systems, according to the ministry.
If Israel is confirmed to have instigated the strikes, it would be the first attack since U.S. President Donald Trump announced last week the withdrawal of American troops from Syria.
Addressing a graduation ceremony for new pilots at an Israeli air force base on Wednesday, Prime Minister Benjamin Netanyahu made no direct reference to specific attacks or Moscow's criticism.
But he reiterated Israel's intention to prevent "Iranian military entrenchment, which is directed against us" in Syria.
"We will act against it, vigorously and continuously, including during the current period," Netanyahu said.