Sunday's reported attack comes days after U.S. officials told CNN that Israel had conducted an airstrike against Syria.
Two U.S. officials told CNN on Friday that Israel apparently launched an airstrike into Syria on Thursday or Friday.
The Israeli military did not comment on the U.S. claim. But Israel has long said it would target any transfer of weapons to Hezbollah or other terrorist groups as well as any effort to smuggle Syrian weapons into Lebanon that could threaten Israel.
"We are watching everything when it comes to the movement of these types of weapons. We have the means to do that," a senior Israeli defense official told CNN's Sara Sidner on Sunday. The official is not authorized to speak to the media.
Shaul Mofaz, a lawmaker in Israel's Knesset, told Israeli Army Radio on Sunday that Israel isn't meddling with Syria's civil war. But Israel must protect itself from Lebanese militants, he said.
"For Israel, it is very important that the front group for Iran, which is in Lebanon, needs to be stopped," Mofaz said.
"Everything that goes into the hands of Hezbollah is not directly related to the rebels. Israel never interfered in the past or today in their actions. Nevertheless, I need to say that Hezbollah is deeply involved up to its neck in what is happening in Syria. Hezbollah helps the Iranians navigate against the rebels."
Hezbollah did not immediately comment after Sunday's claims.
Lebanon's National News Agency reported that Lebanese President Michel Suleiman condemned what he called "Israel's onslaught against Syria." Israel used Lebanese airspace to strike Syria, he said.
Syria: Israel has targeted the defense facility before
In January, Syrian authorities said Israeli warplanes killed two workers and injured five others when they struck the same research facility that officials said was targeted on Sunday.
A U.S. official told CNN at the time that the Syrian claims were false. The official said Israeli fighter jets targeted a Syrian government convoy carrying surface-to-air missiles bound for Hezbollah. But Syria denied there were such shipments.
On Sunday, al Mekdad said details were unclear about what he described as the latest Israeli strike on Syria.
"Until now, the details are not clear on what happened. Did they fire missiles? ... It is not clear for me, because I don't know how it happened, and of course it is worrying, but Israel will suffer the same," the Syrian deputy foreign minister told CNN. "When their agents in Syria were defeated, they are trying to influence from the outside. This is exactly what happened. This is direct Israeli support for al Qaeda ... and the other forces fighting against Syria, to undermine Syria and to weaken Syria."
But an opposition group also condemned what it described as Israeli attacks on the research facility, arguing that the violence shows the weakness of President Bashar al-Assad's government.
"It is clear that the regime, which claims to be an opposing force, is instead weakening Syria in the face of an enemy," the opposition Syrian National Coalition said in a statement.
The opposition umbrella group said it was suspicious of the attack's timing.
"These strikes have given the regime the necessary time to draw attention away from its crimes and massacres on the Syrian coast," the coalition said. "It is not unlikely that as a result of these attacks, and world distraction, more crimes will be committed."
Sectarian violence continues
The latest report of rocket attacks comes as sectarian violence erupted in northwestern Syria. Three consecutive days of killing by mostly Alawite forces have left hundreds of predominantly Sunni residents dead, opposition groups said Saturday.