Sporadic explosions and gunfire continued at Islamabad's Lal Masjid and religious seminary early on Wednesday as Pakistani troops battled the last pockets of resistance by militants.
A day after the start of the storming operation at the city centre complex, military spokesman Major General Waheed Arshad said a handful of defenders were still entrenched in underground positions.
Security forces moved slowly to avoid harming women and children still thought to be held hostage in the premises, he said.
"Only after we comb the buildings after the operation will we be sure of casualty numbers," Arshad said mid-morning after the complex fell quiet.
Amid speculation that a far higher death toll was being withheld to avert a major backlash by extremists and anger among the general public, the official said more than 50 militants had been killed. Nine members of the security forces also died and 28 were wounded.
Hundreds of shrouds for bodies were ordered to the scene as the fighting began winding up Tuesday.
Journalists are expected to be admitted to the badly damaged Lal Masjid mosque and Jamia Hafsa madrassa later on Wednesday.
The body of its slain deputy chief cleric, Abdul Rashid Ghazi, was reportedly removed and taken for post-mortem and DNA testing.
Ghazi died Tuesday afternoon in shooting in one of a series of bunkers in the basement of the seminary. The chief cleric, his brother Maulana Abdul Aziz, was arrested last week while trying to flee the mosque disguised in a burqa.
Remains of Ghazi and four other people killed in the fighting were due to be flown during the day to the brothers' remote home village of Rojhan Mazari in the central Punjab province for burial.
Security measures were stepped up there in anticipation of possible disturbances by supporters of the clerics.
Police were also deployed at two village seminaries built by Ghazi's late father, who also built the Lal Masjid four decades ago, according to a local duty officer.
"So far the situation is under total control," the officer said.
Since the start of the mosque assault, authorities placed police, paramilitary and army units on high alert at major cities and in Pakistan's restive border regions near Afghanistan.
President Pervez Musharraf ordered the storming operation after talks for the surrender of the militant clerics and heavily armed followers failed early on Tuesday.
The standoff began in January when hundreds of stick-wielding female students of the seminary occupied a children's library in Islamabad in protest at the demolition of mosques in the capital.
Emboldened by the inaction of authorities, more students who were demanding the enforcement of Shariah law in Pakistan began an anti-vice campaign in the capital, detaining alleged prostitutes, harassing storeowners and kidnapping policemen.