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Opposition to centre
Opponents of the New York centre building plan say it is insensitive to the families of the victims of the 2001 events.
The New York imam involved in the project, Feisal Abdul Rauf, said on Friday he had no meeting planned with the Florida pastor.
Sharif el-Gamal, project developer for the centre, denied it would be moved.
Obama said at the news conference that he recognised "the extraordinary sensitivities" surrounding the September 11 attacks.
But he said it should be possible to erect a mosque near the so-called Ground Zero site, or a building representing any other kind of religion.
"This country stands for the proposition that all men and women are created equal, that they have certain inalienable rights. One of those inalienable rights is to practice their religion freely," Obama said.
"We are not at war against Islam, we are at war against terrorist organisations that have distorted Islam and have falsely used the banner of Islam," he added.
Former heads of the 9/11 Commission that studied the 2001 attacks presented a 43-page report they called a wake-up call about the radicalisation of Muslims in the United States and the changing strategy of al Qaeda and its allies.
"The threat that the US is facing is different than it was nine years ago," said the report, released by the Washington-based Bipartisan Policy Center.
"The US is arguably now little different from Europe in terms of having a domestic terrorist problem involving immigrant and indigenous Muslims as well as converts to Islam."
US officials have warned that cases such as the threat to burn the Korean could lead to a recruiting bonanza for al Qaeda.