Among those killed in the operation that began Tuesday after hours of negotiations failed to convince the militants to surrender was the mosque's cleric, Abdul Rashid Ghazi. Officials hadn't announced the death toll, but the Voice of America reported about 60 radical Islamic militants and eight soldiers had died.
The radical Islamic students, led by Ghazi, had occupied the mosque for months during which time they kidnapped police officers and others to press their demand for imposition of religious laws in the city.
Pakistani forces met with stiff resistance from those still holed up inside the mosque when the assault began.
The VOA report said some women and children had been rescued but several more inside the mosque remained unaccounted for after the operation.
Separately, the BBC reported Wednesday there were concerns the mosque episode could set off a violent reaction from other radical mosques in Pakistan, which may come to view Ghazi as a martyr opposed to President Pervez Musharraf's government and its support of the United States in the fight against terrorism.