Pakistan says it was looking to eliminate Al-Qaeda number 2 Ayman al-Zawahiri during the air raid on the madrassa at Bajaur in its tribal northwest in which at least 80 people were killed.
Maulvi Liaqat's madrassa was "an isolated terrorists training facility frequently visited" by al-Zawahiri, The News International newspaper said on Wednesday, quoting unnamed officials.
The school was actually used for imparting training to new recruits of second-and third-tier leadership of Al-Qaeda.
The officials showed stills and videos of the early morning training sessions at the destroyed seminary with participants drawn from Pakistan's Swat, Dir and Bajaur and even Afghanistan.
The video and still photos taken through infrared cameras clearly show people between 20 and 30 years carrying out exercises, though no arms or weapons were being used.
The isolated seminary has a large portion for training, an undamaged mosque and spacious living area, said the security source.
It was claimed that these people were to be sent on their mission in Afghanistan and Pakistan within a day or two.
The officials said they were also looking for links between weapons in the seminary and the area and the rockets found last month in the VVIP zone of Islamabad.
They also pointed out that the Bajaur area was under the influence of the Jamaat-e-Islami, which was spearheading the protests by the tribals.
The area was adjacent to Afghanistan's Kunar province, which is the stronghold of former Afghan prime minister Gulbuddin Hekmatyar, who is supporting the Al-Qaeda-Taliban operations against the NATO-led forces in the troubled country.
Meanwhile, in a report from Washington, The News International quoted Pakistan's envoy to US Lt Gen (retd) Mahmud Ali Durrani as denying American media reports that the air strikes constituted an abrupt policy shift by Pakistan.
The American media has indicated a coordinated operation with the US and NATO forces following the trilateral meeting last month between the presidents of the US, Afghanistan and Pakistan.
Durrani insisted that the operation was carried out exclusively by Pakistani security forces and that there was no involvement of the US or the NATO forces that operate across the border in Afghanistan.
However, Durrani maintained that Pakistan was not acting in isolation. "All the three countries had agreed on taking this action," he said.
When asked about the sensitive nature of the operation, the ambassador had earlier told the Washington Post: "Yes, there are sensitivities, but we cannot sit on our haunches and do nothing.
"Many times, things we do in the tribal areas are misinterpreted and not popular. But you have to do tough things. It sends the message that we mean business."
Durrani ridiculed critics at home and in the US that the operation had been "secretive" and that ground operation would have sufficed.
The nature of the operation had to be secretive to prevent information leak and for the same reason it had to be in the form of an air strike to prevent those wanted from fleeing, he said.
Meanwhile, a 20,000 strong rally of tribals was told that suicide squads are being readied to kill on sight any "government spy" and "American spy" found in the tribal area.
Inayatur Rahman, a tribal leader, announced at the rally that he had prepared a "squad of suicide bombers" to target Pakistani security forces in the same way the insurgents are attacking Americans in Afghanistan and Iraq.
"We will carry out these suicide attacks soon," he said,
"Our Jihad will continue and god willing people will go to Afghanistan to oust American and British forces," said Maulana Faqir Mohammad, a pro-Taliban cleric.
Rallies were held in other Pakistani cities, including Karachi, Peshawar, Lahore, Multan, Quetta and Islamabad in protest against the air strike on the madrassa.
The protesters burnt US flags and effigies of President George W Bush, called for the toppling of Musharraf's government and denounced the killing of innocent students and teachers at the madrassa, the newspaper said.