Iraq was braced on Friday for a return to a level of sectarian war last seen almost a decade ago as Shia fighters rushed to Samarra to confront Sunni insurgents and the country's leading Shia cleric called on his followers to take up arms to defend "their country, their people and their holy places"

Convoys of fighters were seen early on Friday being escorted north by Iraqi police trucks from Baghdad to Samarra, the central city where insurgents – led by the Sunni militant group the Islamic State of Iraq in the Levant (Isis) – were in control after a lightning strike south.

The volunteer Shia fighters were quickly assembled after Iraqi forces abandoned their positions in most of the area, leaving only a small number of troops to guard the Imam al-Askari shrines – the two shrines blown up by insurgents eight years ago, triggering the sectarian war that almost destroyed the country.

Hours later a statement from Iraq's most influential Shia cleric, Grand Ayatollah Ali al-Sistani, read to his followers at Friday prayers in Kerbala urged them to take up arms against the Sunni insurgents. "People who are capable of carrying arms and fighting the terrorists in defence of their country … should volunteer to join the security forces to achieve this sacred goal," the statement said.

Samarra is the fourth northern city to have all but fallen out of government control. The embattled prime minister, Nouri al-Maliki, appears to have drawn battle lines further south in Taiji, hoping to defend Baghdad against insurgents who have occupied the north virtually unopposed.

The fast-moving insurgency has emerged as the biggest threat to Iraq's stability since the US withdrawal at the end of 2011.

The UN human rights spokesman, Rupert Colville, said on Friday that hundreds of people were killed, many of them summarily executed, after Isis overran Mosul on Tuesday.

"We've received reports of the summary execution of Iraqi army soldiers during the capture of Mosul and of 17 civilians in one particular street," Colville said, citing the UN mission to Iraq. "There was also the execution of a court employee in the Dawasa area in central Mosul and the execution of 12 people in Dawasa who were believed to have been serving with the Iraq security services or possibly with members of the police."

He said the UN mission had interviewed some of the 500,000 who fled Mosul. A further 40,000 people are were estimated to have fled Tikrit and Samara, according to the International Organisation for Migration.

Barack Obama on Thursday set the stage for renewed US military action in Iraq when he said his national security chiefs were looking at any and every way they could help the Iraqi authorities. White House officials said the president did not envision any circumstances in which ground troops could return to the country. Air strikes, however, are under active consideration.

The US secretary of state, John Kerry, described the crisis as "a real wake-up call" to Iraq's divided political leadership, and urged them to set aside "persistent divisiveness and gridlock".

"We are laser-focused on dealing with the crisis at hand," Kerry said after discussing Iraq with his British counterpart, William Hague, at a conference in London. "Now is the time for Iraq's leaders to come together and to show unity. Political division, fuelled by ethnic or sectarian differences simply cannot be allowed to steal from the Iraqi people what so many have given so much for over the course of these last years."

Describing Isis as "the enemy of decency", Kerry said he did not believe Iran or any other regional power felt it would benefit from the current situation in Iraq.

Military capability within Iraq's government forces was not the issue, he argued: "What has been lacking in Iraq in these last weeks and months has not been a capacity for a trained military to respond, not a lack of numbers to stand up to the 7,000 Isil, but a lack of political will."

He added: "Prime Minister Maliki and all Iraqi leaders need to do more to put sectarian differences aside and to come together in unity and begin being more representative and inclusive."

However, Kerry added, Washington has invested too many troops' lives and too much time and money to back away: "I don't think anybody in the region or in this administration truly believes that it's in the interests of the United States to turn our backs on Iraq."

Heavy clashes had broken out by late Friday morning on the outskirts of Samarra between the Shia volunteers and Sunni insurgents who had been trying to win over residents, some of whom appear to view the new arrivals as liberators.

Witnesses said the shrines remained undamaged so far and that the insurgents had not been menacing residents. "Some of them have long hair and they are carrying black flags," said one man. "They are Arabs from other countries."

The Samarra shrines were twice reduced to rubble in February and April 2006 in attacks that sparked a brutal two-year sectarian war across Iraq. Since then, Shia Islamic sites have remained key targets as Isis-led insurgent groups try to draw the Shia-led government back into the fight.

Meanwhile, Iraqi officials who remained in the northern city of Kirkuk, which was seized by Kurdish peshmerga forces on Thursday, said the Kurds were consolidating their presence.

"They came to stay," said one police captain on Friday. "They're not going anywhere."

The Kurdish control of Kirkuk, a city coveted by them for centuries, is one of the biggest shifts in a week that has starkly exposed the impotence of the government and the frailty of Iraq's borders.

Officials in Baghdad have conceded that the country is at increasing risk of crumbling along ethnic sectarian lines.

Isis has been handing out flyers in the towns it has seized assuring residents who have remained that it is there to protect their interests. The campaign for hearts and minds is gaining some traction, with some residents railing against perceived injustices at the hands of the Shia majority government. But on Thursday it said it would introduce sharia law in Mosul and other towns, warning women to stay indoors and threatening to cut off the hands of thieves. "People, you have tried secular regimes … This is now the era of the Islamic state," it proclaimed.

Iraqi officials estimate the total number of Isis forces in Iraq at around 6,000.