Pastor Terry Jones, of Gainesville's Dove World Outreach Center, said he considered Gen. David Petraeus' concerns "very, very serious" but was still "weighing the situation."
Petraeus had earlier issued a stern warning that burning the Muslim holy book could endanger U.S. troops and Americans worldwide.
Jones said he was praying about the situation and was open to having his mind changed.
"We are definitely weighing the situation," Jones said. "We are weighing the thing that we are about to do, what it could possibly cause, what is our actual message, what are we trying to get across. It's very, very important that America wakes up."
The small evangelical church plans to burn copies of the Muslim holy book on Saturday, the ninth anniversary of the attacks on the U.S. The church has been denied a permit to hold a bonfire but has said it will go ahead with the burning.
"Images of the burning of a Qur'an would undoubtedly be used by extremists in Afghanistan - and around the world - to inflame public opinion and incite violence," Petraeus wrote in an email to The Associated Press.
"I am very concerned by the potential repercussions of the possible [Qur'an] burning. Even the rumour that it might take place has sparked demonstrations such as the one that took place in Kabul yesterday. Were the actual burning to take place, the safety of our soldiers and civilians would be put in jeopardy and accomplishment of the mission would be made more difficult."
The U.S. Embassy in Afghanistan has also condemned the church's plans.
Protests erupt in Kabul, Indonesia
On Monday, hundreds of Afghans demonstrated outside a mosque in Kabul. They burned U.S. flags and an effigy of Jones. The protesters chanted "Death to America," and they briefly threw stones at a passing U.S. military convoy until rally organizers told them to cease.
Demonstrations have also taken place in several cities in Indonesia.
Fifteen people died in riots in Afghanistan in 2005, after Newsweek magazine reported that interrogators at the U.S. detention centre in Guantanamo Bay allegedly flushed a copy of the Qur'an down the toilet in order to provoke inmates to talk. The magazine later retracted its story.
In an article carried Tuesday, the Vatican's newspaper said Christians around the world were protesting the plan to burn the Qur'an.
The headline on the story in L'Osservatore Romano read: "No one burns the Qur'an."
In the article, Archbishop Lawrence John Saldanha of Lahore, Pakistan, described the plan to burn the book as "contrary to the respect owed all religions and against our doctrine and faith."
With files from The Associated Press
