The Syrian army says Israeli war planes fired rockets from Lebanese airspace targeting an army position in a military area near Damascus on February 7.
A statement broadcast by Syrian state television described the airstrikes as “a new Israeli aggression”.
The army destroyed most of the missiles, it said, but did not give details of any damage or casualties.
The Syrian Observatory for Human Rights, a Britain-based monitor of the war, said at least some Israeli missiles had hit military targets near Damascus.
"Syria's air defence system blocked some of the missiles, but others hit ammunition depots near Jamraya," Observatory head Rami Abdel Rahman said.
Jamraya, which lies just over 10 kilometres (seven miles) northwest of Damascus, is home to several military positions and a branch of the Syrian Scientific Studies and Research Center (SSRC).
Jerusalem Post quotes "unofficial media in Syria" that the target of the Israeli attack was an Iranian base in the Jamaraya region.
An AFP correspondent in Damascus heard loud blasts around 3:30 am (0130 GMT).
There was no immediate comment from Israel about the report.
It is the second accusation from Syrian President Bashar al-Assad’s forces in less than a month.
On January 9, Syria’s military accused Israel of launching missiles at military outposts in the area of Qutayfeh in the Damascus countryside, causing damage.
Israeli has carried out numerous air strikes against targets within Syria during the seven-year civil war – often saying the attacks have targeted suspected arms shipments meant to supply Lebanon’s Hizballah militant group, which is fighting alongside Assad’s forces.
The February 7 attack came a day after United Nations war crimes experts said they are investigating numerous reports of alleged chlorine attacks against civilians in rebel-held towns of Syria.
The UN Commission of Inquiry on human rights in Syria said the targets of the alleged chemical attacks were town of Saraqeb in the northwestern province of Idlib and the Douma in the Eastern Ghouta suburbs of Damascus.
Based on reporting by Reuters, AP, AFP, Jerusalem Post and SANA