Syria will "respond immediately" to any new Israeli attack against its territory, its deputy foreign minister told AFP on Thursday, after two reported Israeli strikes on military targets last week.

"The instruction has been made to respond immediately to any new Israeli attack without (additional) instruction from any higher leadership, and our retaliation will be strong and will be painful against Israel," Faisal Muqdad said.

He spoke in an interview with AFP in the Syrian capital.

Senior Israeli sources said the strikes targeted weapons bound for the powerful Lebanese Shiite group Hezbollah, a close ally of Damascus.

Muqdad denied that.

"They absolutely did not achieve their objective and they lied when they said they are targeting Hezbollah," he said.

There is "no way Syria will allow this to happen again," he added.

Israel reportedly targeted military sites near the capital Damascus early on Friday morning and again early on Sunday morning, with at least 42 soldiers reported dead in the second strike.

The Jewish state has repeatedly warned it will intervene to prevent the transfer of advanced weaponry to Hezbollah, with which it fought a devastating 2006 war.

The strikes last week were the third time Israel is thought to have hit sites inside Syria since the beginning of an uprising against the regime of President Bashar al-Assad in March 2011. That first was in January of this year.

The uprising, which began with peaceful protests, has devolved into a bloody conflict that has killed more than 70,000 people, according to the UN, and displaced millions of Syrians.