Syrian security forces were reported to have launched another wave of violence against pro-democracy protesters on Tuesday as President Bashar al-Assad rejected a Turkish appeal to change tack or meet the fate of Libya's Muammar Gaddafi.

Human rights groups recorded at least 40 civilians dead on the day that Ahmed Davutoglu, Turkey's foreign minister, met the Syrian leader to issue what was billed as a "final warning" to end the five-month crackdown, estimated by the US as having claimed 2,000 victims.

Syrian's state news agency, Sana, quoted Assad as telling Davutoglu that he would "relentlessly fight terrorist groups" – the terminology used by Damascus to describe anti-regime protests. Davutoglu returned to Ankara without speaking to reporters but was expected to hold a press conference later.

Activists quoted by al-Arabiya TV said 17 people had been killed on the third day of an assault on the Deir Ezzor, close to the border where many people have links to Iraq and Saudi Arabia.

The Syrian National Organisation for Human Rights reported 26 people killed and dozens wounded when troops backed by tanks and armoured vehicles stormed Soran and other villages north of Hama, target of a 10-day assault to crush protests. Syrian state media said government forces were withdrawing from the city.

The Syrian Revolution Co-ordinating Union said the bodies of two sisters, aged six and 11, were among five brought to a hospital in nearby Tibet al-Imam. Four people were also killed in Binnish, near the border with Turkey.

"The whole town has been joining in night rallies against Assad after Ramadan prayers," a resident said. A member of the Local Co-ordination Committees told the Guardian more than 20 tanks and armoured vehicles had entered the town at 4am, with forces shooting, raiding houses and making arrests, including of teenage boys. "This town has been protesting in huge numbers," said the activist, named Odai. "That's why they [the regime] want to put it down."

Soldiers entering houses had stolen money and jewellery. Similar reports have come from other cities including Homs. Tanks were reported in the northern town of Idlib.

As the violence continued, it was rumoured that Ali Habib, the former Syrian defence minister, had been found dead after being replaced on Monday. But sources in Damacsus insisted that Habib, like the Assads a member of the minority Alawite sect, was unwell but alive.

In the past high-profile Syrians who have fallen foul of the regime have been killed or reportedly taken their own lives in mysterious circumstances. True or not, the story seemed symptomatic of a febrile atmosphere and heightened intense speculation about the inner workings of the Assad regime.

Opposition sources said they were worried that the new defence minister, Daoud Rajah, had been chosen to drive a wedge between his own Christian community and the country's Sunni majority. The appointment was also seen as reflecting possible disagreements the president and his brother Maher, who in effect commands the elite fourth division and has been overseeing the security crackdown.

Turkish officials protested at suggestions Davutoglu was simply delivering a message from the US, after briefing by the state department in Washington about a conversation between him and the secretary of state, Hillary Clinton.

Assad's diplomatic isolation deepened this week after Saudi Arabia led Kuwait and Bahrain in recalling their ambassadors from Damascus in protest at the repression. Diplomats say the US and Britain were instrumental in pressing Arab states to break their silence and change tack. King Abdullah of Saudi Arabia called the Syrian regime "a killing machine".

Emissaries from India, Brazil and South Africa are also due in Damascus to appeal for an end to the crackdown and the introduction of genuine democratic reforms. All three have so far been reticent about stronger UN action against Syria.

Activists in Damascus said they were drawing hope from the escalation of protests and the ratcheting up of international pressure on Assad. But none said they could envisage the way in which the regime would fall.

Human Rights Watch said on Tuesday the UN security council should press Syria to comply with its demand to end attacks against peaceful protesters.

"President Bashar al-Assad needs to hear loud and clear that the security council will not tolerate such contempt for its united call for Syria to change course," said Sarah Leah Whitson, Middle East director at Human Rights Watch.

Russia's foreign minister, Sergei Lavrov, said "precedence should be given to ending the violence and continuing efforts to effect profound political and socioeconomic changes in Syria without delay".

Syria has banned foreign media and restricted local coverage that strays from the official party line, which states the regime is fighting thugs and religious extremists who are acting out a foreign conspiracy.

Nour Ali is a pseudonym for a journalist based in Damascus