In a joint statement, eight human rights groups said 46 people were arrested.
"We condemn this extremely violent and unjustified way the Syrian security services dealt with peaceful rallies in Douma where police used excessive force against demonstrators," said the statement.
The rights groups reported that four people died and dozens were wounded in the crackdown. A human rights activist reported eight dead.
A Douma resident told AFP the agricultural town was calm despite security forces withholding some bodies from the previous day's deadly violence in an apparent bid to prevent funerals from sparking fresh protests.
Families decided against burying four of the dead on Saturday although life in Douma was back to normal, with shops open and a "usual" deployment of security forces.
A witness told AFP security forces used live ammunition to disperse stone-throwing protesters after weekly Muslim prayers on Friday.
The authorities denied the security forces were responsible for the deaths, blaming them on an "armed group" which opened fire from rooftops on both demonstrators and police.
They acknowledged an unspecified number of deaths and said dozens were wounded, some of them policemen.
State television charged that "some of the demonstrators had daubed their clothes with red dye to make foreign reporters believe that they had been injured."
Some 200 people demonstrated outside the courthouse in Daraa, a tribal town near the Jordan border, where security forces arrested eight people between a morning raid and a round-up after the protests, an activist told AFP.
A 20-year-old killed by security forces during a protest in Sanamein, just outside Daraa, was to be buried in nearby Inkhel, a human rights activist said.
He was one among as many as three people killed during Friday's protest in the village. The official SANA news agency said a soldier was also seriously wounded in Daraa itself when young men tried to snatch his weapon.
Security forces carried out a series of raids in the area, another activist said, adding that architect Khaled al-Hassan, lawyer Hassan al-Aswad and teacher Issam Mahameed were among those detained.
Yusef Abu Rumiyeh, a member of parliament for Daraa, denounced security forces for opening fire on his constituents "without pity" and criticised President Bashar al-Assad for not offering his condolences.
The security forces "opened fire on the citizens of Daraa, killing and injuring them and preventing the wounded from getting to hospital," said Rumiyeh, in a video uploaded to YouTube.
"The people of Hauran were waiting for President Assad to visit to offer his condolences. Had he done so, nothing that happened subsequently would have taken place."
In Homs, the Syrian Observatory for Human Rights documented 17 arrests while authorities accused another "armed group" of firing on demonstrators in the industrial city and killing "one girl."
The rights group demanded the release of all prisoners of conscience and political prisoners, and called for measures to ensure the safety of peaceful protest.
Meanwhile, at least 2,000 Druze in the Israeli-occupied Golan Heights demonstrated on Saturday in a show of support for Assad, Israeli news website Ynet reported.
The United Nations and the United States slammed the use of force against peaceful demonstrators in Syria.
UN chief Ban Ki-moon said on Saturday he was "convinced that there is no alternative to an immediate and inclusive dialogue on comprehensive reforms to address the legitimate aspirations of the Syrian people."
In addition to the three cities hit by arrests, "Friday of Martyrs" protests were staged in the port of Latakia, Darriya near the capital and the northeastern Kurdish towns of Qamishli and Amuda.
Washington applauded the "courage and dignity" of demonstrators, urging "all parties to maintain calm and avoid violence" and calling on the Syrian government to allow peaceful demonstrations.
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