In a statement General John R Allen ordered a full investigation.
“When we learned of these actions, we immediately intervened and stopped them,” he said.
Rumours that a Koran had been burned have led to a large protest outside the US air base at Bagram about 60km (40 miles) north of Kabul.
Police told the BBC that at least 1,000 people were taking part in the demonstration and that some elders have gone into the base to talk to Nato officials.
General John R Allen: ‘When we learned of these actions, we immediately intervened and stopped them.’
A BBC reporter at the scene said he saw people crying as they protested at claims that foreign troops had set fire to the Koran, while others threw stones and fire bombs at the security forces.
A photographer for the AFP news agency said that guards at the base fired rubber bullets from a watchtower as the crowd shouted “Allahu akbar, Allahu akbar” (God is great).
‘In his statement, Gen Allen said that the investigation would examine whether troops at Bagram air base “improperly disposed of a large number of Islamic religious materials which included Korans”.