The aerial strike, in which at least 80 people died, has come under growing criticism, with at least one rights group, Human Rights Watch, demanding access to the site and calling for an inquiry.
The Pakistan military says the school in North West province was used by al-Qaeda, but residents say those studying at the religious centre were not involved in any illegal activity.
Days of protests have followed Monday's aerial bombardment.
Major General Shaukat Sultan, Pakistan's chief army spokesman, said on Wednesday that the military had no option but to use helicopter gunships against the school because attempts to arrest people could have led to their escape.
"The biggest factor that contributes to success is surprise," he said.
"If we lost the surprise by 10 minutes, the operation [was] likely to fail."
Sultan said evidence included students in their 20s seen conducting exercises outside the school, school leaders who told rallies they were preparing "suicide bombers" and other intelligence he declined to specify.
Sultan declined to say if those in the school were armed, but said their training made them dangerous.
"We think the response was justified," he said.
The White House supported the raid and praised Pervez Musharraf, the Pakistani president, for showing "determination" to fight terrorism.
"There was a strike and it was intended to go after al-Qaeda," spokesman Tony Snow said.
"And the Pakistani government did it on the basis of intelligence that it had gathered and we support them in this."
Tribal elders, however, said the raid in the Bajur district near the Afghan border set back peace efforts in Pakistan's tribal region.
"There was a strike and it was intended to go after Al-Qaeda. And the Pakistani government did it on the basis of intelligence that it had gathered and we support them in this"
White House spokesman
Abdul Aziz Khan, head of Bajur's council of tribal chiefs, is now demanding a guarantee that there will be no further attacks.
"Without it, we will not begin talks with the government."
At stake is a deal to stamp out militancy similar to that reached in September with tribal chiefs in North Waziristan.
Protests continued on Wednesday for a third day in Bajur, with 10,000 residents and armed activists demanding the death of Musharraf and George Bush, the US president.
In the demonstrations against the US and Pakistani governments more than 20,000 people, many brandishing guns, gathered at several rallies in the remote Pashtun tribal belt along the Afghan border.
The biggest protest was at Salarzae village, near the blown-up school.
Pakistani soldiers have been stopping journalists, human rights monitors and politicians from visiting the site.
Human Rights Watch (HRW), based in New York, urged the government to let independent investigators visit to determine who carried out the attack, how it was planned and executed, and who was killed.
Protesters demanded that the
Pakistani president resign
It also asked the Pakistan government to give journalists and activists access to the shut-off area to establish the facts behind the raid.
Ali Dayan Hasan, the HRW South Asia researcher, said: "The Pakistani government should allow independent investigators into the area to determine who carried out the attack, how it was planned and executed, and who was killed."
Hasan said in a statement: "The onus is on the Pakistani government to provide a credible account of the legitimacy of the attack resulting in the death of so many."