The Florida church's pastor, Terry Jones, said Petraeus' 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."