"The military part of the operation is over. There are no more gunmen inside the mosque," Gen. Waheed Arshad said.
He said the entire complex would now be thoroughly searched to clear any mines and bombs the gunmen may have planted.
According to tentative army reports, 160 students, until recently held hostage, have already been freed.
Female students will be sent home to their parents while all males are being held inside Islamabad's sports complex for an investigation, the military said. The gunmen had earlier insisted that all those remaining in the mosque were there voluntarily and preferred martyrdom to surrender. At least three large buses were parked near the mosque, also known as Lal Masjid, to transport former hostages.
The assault on a religious complex seized by religious hardliners advocating radical Islamic values and wanting to impose Taliban-style rule in the capital July 3 followed the failure to persuade their leader, Abdul Rashid Ghazi, brother of the mosque's chief cleric, to surrender and free about 1,000 religious students kept inside.
Ghazi was killed Tuesday night, and his body was found in a cellar in the mosque surrounded by hard-line followers. His brother, Abdul Aziz, was caught last week trying to leave the mosque dressed in a woman's black burqa. Local media have said that at least 70 students and gunmen and 12 soldiers were killed during the standoff.
