President Assad said it used "humanitarian masks and umbrellas just to implement a certain agenda".
The evacuations were of White Helmets and their families.
Israel says it has carried out an evacuation of members of Syria's White Helmets civil defence group from a war zone in south-western Syria. He did not elaborate on the numbers of those evacuated.
Eight hundred so-called "White Helmets" and their family members had taken refuge in Quneitra, the one small part of southern Syria not already under the control of Russian-backed regime forces.
Russia's Interfax news agency, citing the Russian military, confirmed the same number have been taken by bus to the Idlib zone.
Planning for the evacuation had been taking place for some time but speeded up following a recent North Atlantic Treaty Organisation summit in Brussels.
Despite the intervention, the IDF said that "Israel continues to maintain a non-intervention policy regarding the Syrian conflict".
Israel's firing of the missile interceptors triggered two rounds of rocket alert sirens in communities in the northern Galilee and Golan Heights regions, near the borders with Lebanon and Syria.
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The group are now in Jordan where they have been given temporary asylum.
The group, which operates in opposition-held areas, is often targeted in Syrian government attacks on its members and facilities.
Officially known as Syrian Civil Defense, the "White Helmets" are best known for saving people trapped under rubble after bombings and running search-and-rescue operations to find people lost during battles.
Members of the "White Helmets" civil defence group were among those removed from the country.
The request came as the White Helmets volunteers and their families were threatened by advancing forces of the Syrian government in the south of the war-ravaged country.
The rescue marked the first time in the eight-year war that Israel has allowed Syrians to flee through its territory.
The Israeli army called the move "an exceptional humanitarian gesture", apparently to make it clear that further evacuations were not to be expected.
More than 650,000 Syrian refugees are registered with the UN High Commissioner for Refugees (UNHCR) in Jordan but the kingdom says it hosts 1.3 million Syrian refugees.
"More than half of the evacuees are women and children", said Observatory head Rami Abdel Rahman.
Panicked passengers, fearing for their lives, posted pictures of the militia surrounding their buses on social media.