Syrian forces "in cooperation with the friendly Russian forces carried out precision... air and missile strikes targeting the fortified bases of terrorist organisations" in the Idlib region, the ministry said in a statement carried by state news agency SANA.
The operation came "in response to daily and repeated attacks... on civilians" in residential areas in nearby Hama province, it added.
The bases, which contained weapons, ammunition and drones, were "totally destroyed", according to the statement.
It did not specify the date of the bombardment, but the announcement came a day after Russian air strikes killed eight fighters affiliated with jihadist group Hayat Tahrir al-Sham (HTS), which controls rebel-held Idlib, according to the Syrian Observatory for Human Rights.
Despite periodic clashes, a ceasefire deal brokered by regime ally Moscow and rebel-backer Ankara has largely held in northwest Syria since March 2020.
But the Britain-based Observatory war monitor said the Idlib region, Syria's last opposition bastion, and nearby areas have witnessed an increase in attacks in recent days.
Sixteen civilians and 13 fighters have been killed in attacks by the Syrian regime and Russian forces on Idlib in the past week alone, according to the monitor.
Artillery and drone attacks by the jihadists on regime-held areas have killed six civilians including three children and a soldier in the same period, it added.
On Sunday, Russian air strikes killed at least 13 people in Idlib, in what the Observatory said was the deadliest attack in Syria this year.
At least nine civilians, including two children, were among the dead -- six of them killed at a fruit and vegetable market in Jisr al-Shughur.
In regime areas, one civilian was killed in a drone strike near the Latakia province village of Qardaha, where the family of President Bashar al-Assad hails from, according to the Observatory.
Syria's 12-year war broke out after Assad's repression of peaceful anti-government demonstrations escalated into a deadly conflict that pulled in foreign powers and global jihadists.
The war has killed more than half a million people and displaced millions.
Rebel-held Idlib region is home to about three million people, around half of them displaced.
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