The statement by Foreign Ministry spokesman Jihad Makdessi was the first response to an appeal by U.N.-Arab League envoy Kofi Annan who on Friday urged Syrian authorities to stop military activities first, as "the stronger party" and in a "gesture of good faith."
Makdessi told state TV the military is in these cities "in a state of self defence and protecting civilians."
"The Syrian army is not happy to be present in residential areas," Makdessi said late Friday. "Once peace and security prevail in these areas, the army will not stay nor wait for Kofi Annan to leave. This is a Syrian matter."
Syria's uprising began a year ago with peaceful protests against President Bashar Assad's regime. In the face of a fierce crackdown, the uprising has become increasingly militarized and opposition groups now say their only hope is to drive out Assad.
The U.N. estimates more than 9,000 people have been killed in the fighting.
International opponents of Assad are struggling to pin down a strategy on Syria, even as the peace plan put forward by Annan is failing to get off the ground.
Annan's six-point proposal to end the violence, which has been accepted by Assad, requires the government to immediately pull troops and heavy weapons out of cities and towns, and abide by a two-hour halt in fighting every day to allow humanitarian access and medical evacuations.
"The government must stop first and then discuss a cessation of hostilities with the other side," Annan spokesman Ahmad Fawzi told reporters in Geneva on Friday. "We are appealing to the stronger party to make a gesture of good faith ... The deadline is now."
Assad promised on Thursday to "spare no effort" to make sure Annan's plan succeeds. But he demanded that armed forces battling his regime commit to halting violence as well.
Many Syrians are frustrated at the lack of will for a foreign military intervention and are deeply skeptical Assad will carry out Annan's peace plan, saying the president has accepted it just to win time while his forces continue their bloody campaign to crush the uprising.
The Britain-based Syrian Observatory for Human Rights said that government shelling of some neighbourhoods of the central city of Homs and the nearby town of Talbiseh killed two civilians on Saturday. It added that the bodies of five men, who appear to have been subjected to torture, were found in the northwestern village of Tahtaya.
For the U.S. and its allies, Syria is proving an especially murky conflict with no easy solutions. Assad's regime is one of Washington's clearest foes, a government that has long been closely allied with Iran and anti-Israel groups Hamas and Hezbollah, which the U.S. considers terrorist. Saudi Arabia and other Sunni-led Gulf countries are eager to see Assad's fall in hopes of breaking Syria out of its alliance with their regional rival, Shiite-majority Iran.
"The battle to bring down the state in Syria has already ended and the battle of reinforcing stability has started," said Makdessi, in an apparent reference to recent gains by Syrian troops in their crackdown on the rebels.
U.S. Secretary of State Hillary Rodham Clinton was flying on Saturday from Saudi Arabia, where she held talks with Saudi King Abdullah and others on ways to resolve the Syrian crisis and other regional strategies, to Turkey, ahead of Sunday's 60-nation gathering of the "Friends of the Syrian People" in Istanbul.
The U.S. remains opposed to arming Syria's rebels, which some Gulf states have proposed, even as continued violence is stymying U.N. efforts to persuade Damascus to make good on a cease-fire plan it has accepted.
Bassem Mroue can be reached on twitter at http://twitter.com/bmroue