The burning of Qur’an at a NATO base in Afghanistan advanced the Taliban's cause and any repeat of similar "negligence" by Western forces would be disastrous, the Afghan army chief of staff has warned.

The destruction of the holy Qur’an, which the United States described as unintentional, triggered widespread protests and fatal attacks on US troops by Afghan security forces and heavily strained ties between Kabul and Washington.

"The enemy (Taliban) will enlarge it and make use of it in such a way to instigate everybody," General Sher Mohammad Karimi told Reuters in an interview.

"They took advantage of this incident. They will take advantage." Karimi, sitting in his office at the heavily guarded Ministry of Defence, lamented NATO's failure to grasp the sensitivities regarding Afghanistan's culture and religion during the United States' longest war, now in its eleventh year.

"Those friends who have come here to help us are not doing it the way we asked them too," said Karimi, adding he was "very concerned" by the burning of a truckload of Qur’an at Bagram air base about an hour's drive north of Kabul.

"God forbid if this mistake is repeated there will be a lot of trouble next time."

The Qur’an burnings set back the Western campaign to win the hearts and minds of Afghans in order to weaken the Taliban and force it to negotiate an end to the war. Instead, the Taliban urged Afghans to target foreign military bases and kill Westerners.

Violence spread across the country despite an apology from President Barack Obama from street demonstrations to Afghan security forces turning their weapons on US soldiers.

Two high-ranking US officers working as advisers in the Interior Ministry were shot at point blank range in their foreheads at their desks, reinforcing fears of infiltration by the Taliban, who claimed responsibility.

The attack cast doubt on NATO's plan to shift from large combat formations to an advisory role as the alliance tries to wind down the war and pull out troops by the end of 2014.

US officials have said that the Qur’an were confiscated from prisoners on the base and mistakenly discarded in an incinerator. Afghan labourers found charred remains.

Many Afghans complained the United States and NATO had repeatedly insulted their religion over the years. Muslims consider the Qur’an the literal word of God and treat each copy with deep reverence.

Afghans will never accept US justice for five American soldiers involved in the burning of the Qur’an and could rise up in a "storm of fury" if there is no public trial, a senior cleric said on Saturday.

Karimi said the United States was not expected to hand over the men to Afghanistan. But he called for a trial and insisted that American military leaders ensure that similar incidents never take place again.