The incident was the fifth case since last week in which fighting in Syria has spilled over into Israel, and the first since a US-Russian brokered truce went into effect at sunset yesterday to try and end Syria's war, now in its sixth year.
Israel has largely remained on the sidelines of the fighting, but has carried out reprisals on Syrian positions when errant fire previously landed in Israel.
The Israeli military quickly denied the report, saying that a pair of surface-to-air missiles were fired at its aircraft but missed.
"At no point was the safety of IDF (Israel Defense Forces) aircraft compromised," it said.
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Israeli warplanes have conducted several air raids on Syrian army positions over the past weeks after stray shells hit the Israeli-controlled area.
Israel is also widely believed to have carried out airstrikes on arms shipments said to be destined for the Lebanese militant group Hezbollah, a close ally of the Syrian government.