The destruction of the holy books, 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 Qurans 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 Quran 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 Qurans 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 Quran 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 Quran 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.
One of several blunders
The Quran burning incident was the latest blunder for Washington in Afghanistan. In February, the Pentagon grappled with fallout from a photo showing Marines with what looked like a Nazi SS flag.
In January, Defense Secretary Leon Panetta quickly condemned a video showing what appeared to be US Marines urinating on Taliban corpses.
Karimi said the West had failed to comprehend the far-reaching impact of such images in deeply conservative Afghanistan.
He referred to the Afghan soldier who killed four French troops in eastern Kapisa province in January as an example.
"He said he saw the clip of the urination by the soldiers on the dead bodies. It drove him crazy," said Karimi, 66. "Because in our religion even the enemy, you do not disrespect the dead body."
The killings of the French soldiers prompted President Nicolas Sarkozy to pull out of the war a year earlier in 2013.
Any other Western countries following suit would worry Karimi, who graduated from Britain's prestigious Sandhurst military academy and also studied in Russia and Egypt.
Karimi said Afghan security forces, who are largely illiterate and have minimal training, have come a long way. But he stressed they were still highly dependent on Western air support, artillery and intelligence in the war against a resilient Taliban.
Karimi expressed concerns that the United States may want to cut the size of the Afghan army and security forces to reduce funding.
Afghanistan wants to build up security forces to about 350,000, while a Western proposal has been floated for a much smaller size of about 230,000.
"My question to the international community is that you spent billions of dollars to build the Afghan National Security Forces. Now, for a few million dollars, you should not jeopardise ten whole years of achievement," said Karimi.
"If that is reduced, it's just a big gamble with the enemy."
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Is that really necessary to mention? I mean how "lightly guarded" is YOUR ministry of Defence? You even have armed men guarding your Mosque's doors.
Where are the other muslims? why the same protects in Saudi Arabia, Iran, Pakistan, Bangladesh etc?.