General David Petraeus said the planned torching of Islam's holy book would be a propaganda coup for the Taliban in Afghanistan and stoke anti-US sentiment across the Muslim world.
The Dove World Outreach Center at Gainesville, Florida says it will burn copies of the Koran on this weekend's ninth anniversary of the September 11 airborne attacks in protest at what it calls "the evil of Islam".
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In an interview with Tuesday's Wall Street Journal, Petraeus said of the event: "It could endanger troops and it could endanger the overall effort.
"It is precisely the kind of action the Taliban uses and could cause significant problems. Not just here, but everywhere in the world we are engaged with the Islamic community," he said.
The planned protest by the 50-member Florida congregation -- whose Facebook page bears the motto "Islam Is Of The Devil" -- has already triggered outrage in Indonesia, the world's largest Muslim-majority country.
In late August about 100 Indonesian Islamists demonstrated outside the US embassy in Jakarta and threatened "jihad" or holy war if the US Christian group went through with the event.
Alleged desecration of the Koran by US troops in both Afghanistan and Iraq has been an incendiary issue in the past, including when a US soldier deployed to Iraq riddled a copy of the holy book with bullets in 2008.
A subsequent demonstration by about 2,000 people in central Afghanistan turned violent, with a Lithuanian soldier and two civilians killed in an exchange of gunfire between protestors and police.
The Florida church's pastor, Terry Jones, said Petraeus's concerns were "legitimate".
But in a statement to the Wall Street Journal, he added: "We must send a clear message to the radical element of Islam. We will no longer be controlled and dominated by their fears and threats."
Interviewed by AFP in July, Jones said: "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."
