"While these operations were being carried there was intense firing from the militants," he said. The unit commander was killed and one commando wounded.
Abdul Rashid Ghazi, the cleric leading Lal Masjid's Taliban-style movement, told Pakistani television channels more than 300 followers, mostly female students, were killed in overnight gun battles.
Mohammad Ali Durrani, the Pakistani i
nformation minister, said Ghazi was lying.
Hundreds of troops have been surrounding the Lal Masjid, or Red Mosque, in Islamabad since Tuesday when clashes between the armed students and security forces began after months of tension.
Security forces have not mounted a full-scale assault on the compound because of fears for the safety of hundreds of women and children who the government says are being held as human shields.
Instead, troops have been blasting holes in the wall to provide escape routes for those inside.
Ghazi has refused to surrender, saying he would prefer "martyrdom". He also rejected the accusations he was holding women and children as human shields.
Fifty to 60 fighters were believed to be leading the fighting, officials said.
Water, gas and power to the mosque were cut and food was said to be running short. Security forces have occupied another city madrassa linked to the Lal Masjid.
Ghazi said he and his followers would lay down their weapons but would never accept arrest.
About 1,200 students left the mosque after the clashes began but only about 20 have come out since Friday.
Waheed said some had slipped out of the breaches troops were making.
Officials said they did not know how many people remained inside but there could be up to 2,000.
In a related development, four Pakistani soldiers were captured by unidentified armed men in the tribal Bajur district, near the border with Afghanistan, Al Jazeera's Islamabad reporter quoted Pakistani security sources as saying.
The armed men are believed to be pro-Taliban and al-Qaeda elements who have recently threatened to target the Pakistani army to avenge the ongoing incidents in the Red Mosque, the reporter said.
Source: Al Jazeera and agencies