The tinderbox situation in Afghanistan threatened to ignite yesterday as fresh violence hit the country, and it emerged that a former policeman suspected of killing two US Nato officers in Kabul's interior ministry on Saturday spent two months at a religious school in neighbouring Pakistan before the attack.

Protests continued in Afghan cities and spread to Pakistan yesterday after the US admitted that copies of the Koran were accidentally burned by US forces at Bagram airbase.

The worst trouble was in Kunduz province, where a peaceful rally turned violent as marchers tried to enter the district's largest city.

Amanuddin Quriashi, the district administrator, said some in the crowd fired at police and threw grenades at a US base on the city's outskirts. Seven Nato troops were wounded and one protester died when soldiers fired back from the US base. Another protester was killed by Afghan police.

The renewed attacks on Western forces came as the Afghan interior ministry said one of its employees was suspected of killing the two US officers on Saturday.

Abdul Saboor, a former police officer from Parwan province, is in his mid-20s and was working as a driver at the ministry. He fled after the attack and has yet to be traced, despite an extensive manhunt. The Taliban said it carried out the assassinations.

Mr Saboor joined the police force two years ago but was sacked because of absenteeism. He rejoined the interior ministry two months ago.

While he was unemployed, he is thought to have spent two months studying at a madrassa in Pakistan. His identification pass gave him access to the ministry headquarters and before the murders he was spotted on the top floor of the building where the two advisers had their office, close to the Command and Control Centre.

The two Americans – thought to be a colonel and a major – were found dead in their office with gunshots wounds to the head.

President Hamid Karzai appeared on television again yesterday to appeal for calm in the aftermath of the burning of the Koran. Since reports emerged on Tuesday that religious material was mishandled at Bagram, deadly protests have swept the country, leaving 29 people dead and 300 injured.

One of the dead was identified yesterday as Joshua Born, one of two US military policemen who were killed on Thursday by an Afghan soldier serving with the Nato-led International Security Assistance Force (Isaf).

Protests continued yesterday for the sixth consecutive day with peaceful demonstrations in the provinces of Panjshir, Paktika, Maidan Wardak and in Ghazni. However, five officers and two civilians were injured when groups of people threw rocks at the police in Samangan province.

Mr Karzai said that while the "emotions of our people" about the burning of the Koran were "legitimate and valuable", Afghans should try to be calm because it would stop "enemies of our peace and stability" from taking advantage of the situation and from harming people and property.

The Taliban claimed responsibility for Saturday's attacks, saying that they were in revenge for the Koran burning. A statement issued by the group's spokesman, Zabiullah Mujahid, identified the killer as Abdul Rahman and said he had killed four Americans with the help of an accomplice who had helped him to get inside the ministry. The Taliban frequently exaggerates its claims of victory.

The Isaf commander, General John Allen, announced an investigation into the murders, saying the perpetrator was "a coward whose actions will not go unanswered". He met the Afghan Interior Minister, Bismillah Khan Mohammadi, who promised to co-operate with the inquiry.