A bomb blast hit the capital of war-torn Syria and a "terrorist" was arrested, state media said, in a rare attack in the city that has been largely insulated from violence in the country.

The explosion came as another bomb in the northern city of Afrin killed three people and wounded nine others, according to a war monitor, on the first anniversary of a Turkish offensive on the Kurdish-majority region.

Israel has also said it intercepted a rocket fired from Syria after Damascus accused the Jewish state of carrying out air raids on the south of the country.

State news agency SANA said a "bomb blast" had hit southern Damascus "without leaving any victims".

"There is confirmation of reports that a terrorist has been arrested," it said.

The Britain-based Syrian Observatory for Human Rights war monitor reported, however, a "huge explosion" near a military intelligence office in southern Damascus that left a number of people dead and wounded. 

"The explosion took place near a security branch in the south of the city," and was followed by shooting, said the monitor which relies on a network of sources inside the country.

"There are some people killed and injured but we could not verify the toll immediately," it added.

It was unclear if the blast was caused by a bomb that was planted or a suicide attack, according to the monitor.

There was no immediate claim of responsibility.

Syria is locked in a civil war that has killed more than 360,000 people and displaced millions since a brutal crackdown on anti-government protests in 2011 spiralled into full conflict.

With key military backing from Russia, President Bashar al-Assad's forces have retaken large parts of Syria from rebels and jihadists, and now control almost two-thirds of the country.