Syria defied Arab isolation and mounting international anger on Monday as President Bashar al-Assad's security forces continued attacks on pro-democracy protesters across the country.

The US secretary of state, Hillary Clinton, urged al-Assad to return his troops to barracks and release all prisoners, one of the bluntest demands yet made of the Syrian leader, after regional powerhouse Saudi Arabia led a rare chorus of Arab states in condemning the repression.

Reports from Deir al-Zor described artillery and heavy machinegun fire and snipers on roofs as troops and intelligence agents carried out mass arrests in the north-eastern city. On Sunday, 42 people were killed there, nudging the death total during five months of the uprising to more than 2,000.

In Hama, security forces were reported to have deployed an anti-aircraft gun to fire on civilians, diplomats said. Videos from around the country purported to show gunfire, shelling and corpses from violence over the weekend. Three people were reported to have been shot during a funeral in Deraa.

In a political development, al-Assad announced the replacement of his defence minister, Ali Habib, a member of the minority Alawite community, by the army chief of staff, Daoud Rajha, who is a Christian. Analysts said the move seemed intended to emphasise the regime's claim to be defending all Syrian citizens against a sectarian conflict it says is being fomented by Islamic extremists.

State TV described Habib as being in poor health and said the decision to replace him had been taken after consultations by the president.

Syrian media scorned moves by Saudi Arabia and its Gulf allies to protest against the violence by withdrawing their ambassadors from Damascus. The Sana news agency quoted an unnamed official as expressing "regret" that Arab states had "completely ignored facts on the killing and sabotage committed by armed terrorist groups".

Kuwait and Bahrain followed the Saudis in recalling their envoys for consultations.

On Sunday, King Abdullah of Saudi Arabia condemned the crackdown in a speech that was billed as historic but was largely prompted, western diplomats said, by US pressure. Britain has also been lobbying the Saudis and other Arab states, which rarely criticise each other in public, to get tough with Syria.

Qatar, which pursues more independent policies, recalled its ambassdor from Damsacus last month. On Sunday the Arab League, which represents all Arab states, had spoken out for the first time and called on the Syrian authorities to stop acts of violence against civilians.

Speaking on state TV, commentator Samir Shehadi warned that Syria would in future support Shia protestors in Saudi Arabia and Bahrain in retaliation for their stand. Neighbouring Jordan also expressed concern for the first time.

British diplomats said they were alarmed by the arrest of a leading dissident, Walid al-Bunni, and his sons, who had been due to take part in an opposition conference. A leading human rights lawyer was also reportedly detained.

Communications were patchy and details incomplete, but the Syrian Observatory for Human Rights quoted residents in Deir al-Zor as saying that security forces had shot dead a mother and her two children who were fleeing the assault.

"The army opened up with heavy machine guns on al-Joura district. Security forces then launched a search sweep, terrorising residents," an activist in the city told AFP. People were said to be too terrified to take the wounded to government hospitals, instead treating them at home or in makeshift hospitals.

Troops also entered Maarat an-Numan in the northern province of Idlib at dawn on Monday, opposition activists said.

Turkey's foreign minister, Ahmet Davutoglu, is due to meet Assad in Damascus on Tuesday and will be carrying Clinton's message to Assad to release all detained protesters, establish a new government and send his army back to barracks, Turkish media reported.

Bouthaina Shaaban, Assad's media adviser, said Davutoglu would hear a protest that his country had failed to "condemn the brutal killing and crimes committed by the armed terrorist groups".

William Hague, the foreign secretary, condemned the latest violence against Syrians. "This brutality exposes the regime's claims to be committed to a reform process as an utter sham," he said in a statement.

On Sunday night reporters were taken on a tour of the government-run hospital in Hama, where more than 150 fatalities have been reported in recent days, and shown the remains of 16 people, some decomposing. Dr Mohammed al-Omar said most of the bodies were members of the security forces who were killed by armed groups.

Condemnation of the Syrian government spread to the internet, where the hacking group known as Anonymous claimed credit for vandalising the Syrian military's website. The site quickly became unavailable, but screenshots circulated online showed the group's trademark headless suit and a message addressed to the Syrian people saying that "the world stands with you against the brutal regime."