General David Petraeus told The Wall Street Journal on Tuesday that the planned torching of Islam's holy book would feed anti-US sentiment across the Muslim world and be a propaganda coup for the Taliban in Afghanistan.
Afghanistan, where Petraeus leads a 150,000-strong US-led Nato force against an extremist Taliban-led insurgency, is a deeply devout Islamic country. Actions seen by Afghans as against their religion or even suggestions that Western troops have insulted the Koran have led to deadly violence in the past.
In January seven tribesmen were killed by gunfire from Afghan security forces trying to disperse angry crowds during a demonstration sparked by allegations that US troops had torched the Muslim holy book.
An investigation later found that the Koran had not been desecrated.
The Dove World Outreach Center at Gainesville, Florida, says it will burn copies of the Koran on Saturday's ninth anniversary of the September 11 attacks in protest of what it calls "the evil of Islam".
Petraeus said that action would not only jeopardise troops, but harm the overall effort in Afghanistan.
"It is precisely the kind of action the Taliban uses and could cause significant problems," he told the Wall Street Journal. "Not just here but everywhere in the world we are engaged with the Islamic community."
On Monday about 200 men gathered near a mosque in the capital Kabul to protest the planned burning, shouting "death to America" and "long live Islam" for about an hour after their midday prayer, according to witnesses.
The Florida church's pastor, Terry Jones, said Petraeus' concerns were "legitimate," but told the Wall Street Journal his church wanted to send a clear message to Muslim extremists. "We will no longer be controlled and dominated by their fears and threats," he said.
In July, Jones told AFP: "Islam and Sharia law was responsible for 9/11. We will burn Korans because we think it's time for Christians, for churches, for politicians to stand up and say 'no': Islam and Sharia law is not welcome in the US."