Shaykh Abdallah Adhami said Friday in a joint statement with the center's developer that he will no longer serve as a religious adviser to the center.
"It is important for me now to devote my time to the completion of my book, which assists English readers in understanding and facilitating the language of the Quran. I wish the project leaders well," Adhami said.
The 44-year-old had been announced as the new imam on Jan. 14, after its co-founder, Imam Feisal Abdul Rauf, was given a reduced role.
Rauf had been the public face of the center but hadn't always seen eye to eye with its developer, Sharif El-Gamal. Rauf also spent much of his time traveling, often to far corners of the globe, and El-Gamal said he preferred to have someone leading religious programming who could spend more time on building a local congregation.
Adhami was to have been one of several New York City imams fulfilling that role, but shortly after his appointment, news reports questioned his views on homosexuality. In one recorded lecture, he said he believed that homosexuality was linked to childhood abuse.
That prompted El-Gamal to issue a statement last month in which he said that Adhami would not be a leader of the center, called Park51, but just one of a number of religious figures invited to participate in programing.
"The opinions voiced by this diverse group of advisers will not always represent the official position of Park51," El-Gamal said at the time.
In the statement he released Friday announcing Adhami's departure, El-Gamal made no mention of a rift over his beliefs on homosexuality. He said he still hoped Adhami would continue to lead prayers at the facility from time to time.
"We have been humbled by Imam Adhami's contributions to this project over the past few months. His teachings and scholarly work on the Islamic faith remain an important part of our community," the statement said.
The planned Islamic center would sit two blocks from the rebuilt trade center and 9/11 memorial, on a site now occupied by a former clothing store that has been converted into a mosque.
Critics have assailed the center as an insult to the victims of the 9/11 attacks. They say it is inappropriate to build an Islamic institution so close to the site of an attack by Muslim fanatics.
Plans for the center call for it to include a health club, a daycare center, a swimming pool, gallery space, an auditorium, offices and a two-level, below-ground prayer space with room for a congregation of 1,000.