He said it was critical that Americans "not back away" from completing the project.
"The wonderful outpouring of support for our right to build this community center from across the social, religious and political spectrum seriously undermines the ability of anti-American radicals to recruit young, impressionable Muslims by falsely claiming that America persecutes Muslims for their faith," he wrote. "These efforts by radicals at distortion endanger our national security and the personal security of Americans worldwide."
The comments published in the Times were among Rauf's most extensive on the Islamic center since national leaders began weighing in on the debate earlier this year.
For months, the debate has focused on whether the plans for the center would include a mosque just blocks north of where Islamic extremists destroyed the World Trade Center and killed nearly 2,800 people on Sept. 11, 2001.
Opponents say the mosque should be moved farther away out of sensitivity for the families of 9/11 victims; supporters say religious freedom should be protected.
For the past two months, Rauf has been traveling abroad, including taking a 15-day trip paid for by the U.S. Department of State to promote religious tolerance in the Middle East. While on the trip, he occasionally spoke about the center, mostly to local Arab media. He returned to the United States on Sunday.
In the op-ed piece, he explained his reasons for not speaking out more and sooner, saying he felt it would "not be right to comment from abroad."
"It would be better if I addressed these issues once I returned home to America, and after I could confer with leaders of other faiths who have been deliberating with us over this project," he wrote. "My life's work has been focused on building bridges between religious groups and never has that been as important as it is now."
In the nearly 1,000-word op-ed, he outlined his vision for the center, referring to it as a "shared space" for the community that will include "a multifaith memorial dedicated to victims of the Sept. 11 attacks."
"I am very sensitive to the feelings of the families of victims of 9/11, as are my fellow leaders of many faiths," he wrote.
Rauf is one of the directors of the nonprofit organization that was recently formed to raise money for the divisive lower Manhattan project, sometimes known as Park51. The imam referred to the project as the "Cordoba House" in his op-ed piece.
"I know there will be interest in our financing, and so we will clearly identify all of our financial backers," he wrote.