President Pervez Musharraf says he is determined that extremism and terrorism will be eradicated in Pakistan.
He was speaking in a televised address to the nation after officials said 75 bodies had been found at the radical Red Mosque in Islamabad.
Troops launched a 36 hour attack on the mosque early on Tuesday to flush extremists out of the mosque complex.
For months clerics and students had been defying the authorities in their campaign for Sharia law in the capital.
Students had kidnapped police as well as Islamabad residents they considered to be engaged in un-Islamic activity.
'Madrassa a fortress'
Gen Musharraf praised Pakistan's security forces for freeing the Red Mosque in Islamabad "from the hands of terrorists".
"Unfortunately we have been up against our own people... they had strayed from the right path and become susceptible to terrorism."
"What do we as a nation want?" President Musharraf asked. "What kind of Islam do these people represent?"
"In the garb of Islamic teaching they have been training for terrorism... they prepared the madrassa as a fortress for war and housed other terrorists in there.
"I will not allow any madrassa to be used for extremism."
Gen Musharraf said those members of the military who died had given their blood for the country.
He insisted that his government had acted with restraint and had acted only when negotiations had broken down.
A short while earlier, officials said the bodies of 19 people, charred beyond recognition, were among the 75 bodies found in the mosque complex, which includes a religious school for women and girls.
An army spokesman said five of the charred bodies were of people killed by a suicide bomber in a locked room.
There are fears women and children may be among the victims but immediate confirmation is impossible.
Ten soldiers were killed in the operation. Officials say one suicide bomber was inside the buildings.
'Any gender, any age'
"We recovered the head of the suicide bomber and his body parts," said army spokesman Maj Gen Waheed Arshad.
RED MOSQUE STAND-OFF
3 July: Clashes erupt at mosque, 16 killed, after long student campaign for Islamic Sharia law
4 July: About 700 students leave mosque, now besieged by security forces; mosque leader caught trying to flee wearing woman's burka
5 July: More than 1,000 students surrender to security forces
6 July: Women are allowed to leave the mosque; students' deputy leader says he would rather die than surrender
8 July: Ministers say wanted militants are holding women and children inside the mosque
9 July: Negotiators talk to mosque leader via loudspeaker without progress; three Chinese workers are killed in Peshawar over siege
10 July: Pakistani troops storm mosque after failure of talks; army says Ghazi killed
11 July: Pakistani army says all militants cleared from mosque
"We also found five bodies that were burned beyond recognition."
He said another 13 bodies were found that were also so badly charred they could be "any gender, any age".
Military officials said they have taken photographs, fingerprints and DNA samples from the 75 bodies they say were found at the Red Mosque, or Lal Masjid.
Most of the bodies were buried Thursday morning in temporary graves identified with numbers.
An Islamabad city official said at least two children were among 69 bodies buried on Thursday.
The BBC's Barbara Plett says the girls' school, or madrassa, suffered the most damage.
Walls are covered with bullet holes and shattered glass lies everywhere, she says.
The cleric who led the last days of resistance in the mosque, Abdul Rashid Ghazi, was buried on Thursday in his home village of Basti Abdullah in Punjab province in front of hundreds of mourners.
Our correspondent says many Pakistanis supported the operation, saying the government had no choice but to confront the Islamic extremists.
But, she adds, the authorities fear a violent reaction from other radicals and the country is on high alert.
Attacks said to be linked to the mosque assault continued on Thursday in Pakistan's volatile north-west, where support for the Taleban is strong.
In the tribal area of North Waziristan near the Afghan border, a suicide bomber killed himself and two government officials in the town of Miran Shah, police said.
Further north in Swat district, at least five people, three of them police, were killed in a suicide car bombing, officials said. At least one of those killed was reported to be the bomber.
THE RED MOSQUE SIEGE
1 Special forces attack compound from three sides and breach mosque walls
2 Fierce fighting between military and militants on mosque roof
3 Military take control of mosque and clear building
4 Militants fire from mosque minarets as action switches to madrassa
5 Remaining militants holed up in its basement, with women and children