NEW YORK — Federal prosecutors took steps Thursday to seize four U.S. mosques and a Fifth Avenue skyscraper owned by a nonprofit Muslim organization long suspected of being secretly controlled by the Iranian government.

In what could prove to be one of the biggest counterterrorism seizures in U.S. history, prosecutors filed a civil complaint in federal court against the Alavi Foundation, seeking the forfeiture of more than $500 million in assets.

The assets include bank accounts; Islamic centers consisting of schools and mosques in New York City, Maryland, California and Houston; more than 100 acres in Virginia; and a 36-story glass office tower in New York.

Confiscating the properties would be a sharp blow against Iran, which has been accused by the U.S. government of bankrolling terrorism and trying to build a nuclear bomb.

A telephone call and e-mail to Iran's U.N. Mission seeking comment were not immediately answered.

John D. Winter, the Alavi Foundation's lawyer, said it intends to litigate the case and prevail. He said the foundation has been cooperating with the government's investigation for the better part of a year.

"Obviously the foundation is disappointed that the government has decided to bring this action," Winter told The Associated Press.

It is extremely rare for U.S. law enforcement authorities to seize a house of worship, a step fraught with questions about the First Amendment right to freedom of religion.

The action against the Shiite Muslim mosques is sure to inflame relations between the U.S. government and American Muslims, many of whom are fearful of a backlash after last week's Fort Hood shooting rampage, blamed on a Muslim American major.

"Whatever the details of the government's case against the owners of the mosques, as a civil rights organization we are concerned that the seizure of American houses of worship could have a chilling effect on the religious freedom of citizens of all faiths and may send a negative message to Muslims worldwide," said Ibrahim Hooper, spokesman for the Council on American-Islamic Relations.

The mosques and the skyscraper will remain open while the forfeiture case works its way through court in what could be a long process. What will happen to them if the government ultimately prevails is unclear. But the government typically sells properties it has seized through forfeiture, and the proceeds are sometimes distributed to crime victims.