The burning was carried out by pastor Wayne Sapp under the supervision of Terry Jones, who last year drew condemnation over his aborted plan to ignite a pile of the Islamic holy books to mark the anniversary of the September 11, 2001 attacks.
Jones was widely pilloried for his threats to carry out the Quran burning, including by US President Barack Obama.
The foreign ministry condemned the desecration of the Quran as "despicable act."
"There could be no justification for such acts," the ministry said.
"This has deeply hurt the feelings of the people of Pakistan and Muslims all over the world."
The U.S. ambassador to Pakistan Cameron Munter alsocondemned the burning of a copy of Koran in Florida.
"The deliberate destruction of any holy book is an abhorrentact," he said in a statement.
"This is an isolated act done by asmall group of people that is contrary to American traditions."
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