Russia's Defense Ministry said Wednesday that the airstrike in Syria attributed to Israel "directly endangered" two civilian flights.

The ministry did not specify which flights had been threatened but said one of the flights was landing in Beirut and the other in Damascus. It added that Syrian air defences had destroyed 14 of 16 Israeli missiles launched against unspecified targets near Damascus by six Israeli F-16s on Tuesday.

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A Defense Ministry spokesman said the Syrian military didn't fully engage its air defense assets to avoid accidentally hitting the passenger jets. He added that Syrian air traffic controllers redirected the Damascus-bound plane to the Russian air base in Hemeimeem.

>> Israel's extensive Syria strike signals: Business as usual despite Trump and Putin | Analysis

Meanwhile, Prime Minister Benjamin Netanyahu alluded to Israel's activity in the north, saying Israel will not allow an Iranian entrenchment in Syria. "We will act against it vigorously and continuously including during the current period," he said at an Israel Air Force graduation ceremony.

"In the history of the Middle East, there has never been aerial activity such as this. Aircraft ascend and descend, take off and land, and reach arenas both near and far, very far."

According to Netanyahu, U.S. President Donald Trump's decision to pull out of Syria "does not change our policy. We stand by our red lines in Syria and anywhere else."

Lebanon's Foreign Ministry responded to the alleged Israeli air raids later on Wednesday, saying the strikes posed a danger to commercial air traffic that could have caused a major civil aviation disaster.

Foreign Minister Gebran Bassil has instructed Lebanon's envoy to the UN to submit a complaint to the Security Council against the "dangerous Israeli violations that threaten stability in the region," the foreign ministry said in a statement.

Israeli aircrafts struck an arms depot west of Syria's capital city of Damascus from Lebanese airspace, Syrian state media reported Tuesday. According to reports, three Syrian soldiers were wounded in the attack which targeted Hezbollah depots.

A report in the American weekly Newsweek said several senior Hezbollah officials were wounded in the alleged attack.

Citing a Department of Defense source familiar with the details of the attack via senior Israeli representatives, the report said Israeli aircrafts struck a few minutes after the officials had gotten on board a plane to Iran.

However, former director of Israeli Military Intelligence, Maj. Gen. (res.) Amos Yadlin said on Wednesday it is unlikely Israeli had directly struck Hezbollah officials.

Speaking on Israeli army radio, Yadlin said "the probability (of the report) is very low," adding that "we're trying to piece the picture together, with the official Israel remaining silent. We're trying to understand what's been attacked and what were the results of the attack. We're relying on statements from the Syrians and leaks for the Department of Defense."

Although Russia and Israel established a system to avoid friction between Israeli aircraft operating in Syria and Russian military planes in the area, a Russian aircraft was downed by Syrian anti-aircraft missiles during an Israeli airstrike in September. The Russians blamed Israel for the mishaps, a claim that Israel vigorously denied. Russia announced it had delivered the S-300 air defense system to Syria in October following the incident.