Afterwards, some 3,000 people gathered in front of the house of the new governor, Samir Othman al-Sheikh, to "demand an end to the killing," he said.
Earlier, residents were out in the streets trying to prevent security forces carrying out arrests, he said.
In Qatana, 25 kilometres (15 miles) south of Damascus, security forces armed with machine guns and other weapons arrived in the town in pickup trucks overnight and carried out the arrests before searching for more protesters.
The sweep came as people took to the streets of Damascus and Qatana to protest after security forces killed 11 people on Wednesday in Kanaker, 50 kilometres southwest of the capital, said human rights activists.
Among those said to have been detained were two prominent members of a national coordination committee for democratic change, the Observatory said.
"Security forces ... arrested two known Syrian opposition figures Adnan Wehbe and Nizar al-Samadi," it said, adding that their fate "remains unknown."
Webhe is a leader of the Democratic Socialist Arab Union Party while Samadi is a well-known Islamic personality from Douma, a protest hub in Damascus's outer suburbs.
Around another 100 people were arrested overnight in raids on houses in Damascus, the London-based Observatory told AFP in Nicosia by telephone.
"A demonstration was held on Wednesday night on Khaled Ben al-Walid Avenue in Damascus, bringing together many young men and women who blocked the avenue for a short time," said the Observatory.
Protests also took place after evening prayers in Qatana in support of Kanaker, a town of 250,000 people west of Damascus where forces killed 11 people on Wednesday, including a child aged seven, the activists said.
"The military erected a checkpoint at the entrance of Qatana where two tanks were stationed," said the Observatory.
State media quoted officials as saying that "law enforcement agents hunted for armed terrorist gangs that have been terrorising the peaceful citizens of Kanaker."
"Four armed terrorist fighters were killed and two others were wounded in this successful and quality operation," government newspapers reported.
Syria has since March 15 been shaken by an unprecedented revolt against the regime of President Bashar al-Assad which accuses "armed terrorist groups" of wanting to spread chaos in the country.
Despite the ongoing crackdown, Facebook group The Syrian Revolution 2011, a motor of the protest movement, has called on people who have remained silent so far to mass Friday for yet more anti-regime demonstrations.
Security forces have arrested almost 3,000 people in the crackdown on the pro-democracy movement, which broke out in mid-March inspired by regime-changing revolts in Tunisia and Egypt.
"Avaaz has today revealed the identities of 2,918 Syrians who have been arrested by Syrian security forces and whose whereabouts are now unknown," the non-governmental organisation said.
"The in-depth survey conducted by Avaaz estimates that one person is disappearing every hour.
"In the past week alone there have been more than 1,000 arrests and the number of enforced disappearances has been rapidly rising on a daily basis, as the regime steps up its efforts to repress dissent in the build-up to Ramadan," said Avaaz.
Executive director Ricken Patel said that, "hour by hour, peaceful protesters are plucked from crowds by Syria's infamously brutal security forces, never to be seen again."
Avaaz said 1,634 people have died in the crackdown, 26,000 have been arrested, of whom 12,617 are still in detention.
The group said it is establishing a website with photos and brief descriptions of those who have disappeared which would be regularly updated.
It added that it has been collaborating with two credible Syrian human rights organisations to collect the names and photos of each disappeared case "to ensure the list of names is wholly verified."
Meanwhile, the powerful Lebanese militant group Hezbollah on Thursday denied accusations it is assisting the Syrian government to crush protests roiling the country.
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