"I would not say that they are following the teachings of the Prophet, but the warped version of their warped clerics"
Chris, Stockholm, Sweden
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"As far as a figure of militants is concerned the information I have from troops carrying out the operation is around 40," major-general Waheed Arshad, the chief military spokesman, told reporters.
"Three security officials are shaheed [martyred], 15 injured," he added.
Al Jazeera's Rageh Omaar said the mosque compound is a large and complex building which will take the military a long time to cover, in the attempt to combat the armed students.
The army will have to go room by room in a thorough search of those still inside the mosque.
He added that there was no sign of the armed
students giving themselves up.
Earlier on Tuesday Pakistani forces stormed the mosque compound in the capital after negotiations to an end a bloody standoff broke down.
Arshad said security forces launched an operation at 4am (23:00 GMT on Monday) "to clear the madrasa of militants".
"The militants are using small arms and grenades. They are in the basement, we have covered the rooftop," he said, adding that the operation was expected to take three or four hours.
Chaudhry Shujaat Hussain, a former prime minister and ruling party leader who led negotiations with those inside, said the final effort to secure a peaceful solution had failed.
"I am returning very disappointed," he said.
Al Jazeera's Kamal Hyder said Pakistani officials had been hoping for a peaceful end to the seven-day standoff at the Islamabad mosque after negotiators offered religious leaders inside a deal.
The deal was believed to have been arranged after Hussain met Pervez Musharraf, Pakistan's president.
Hyder said Hussain had gone back to the mosque with an offer of safe passage, one of the demands of Abdul Rashid Ghazi, the mosque's deputy leader.
Security forces had previously held back from mounting a full-scale assault because of fears for the safety of women and children that they said were being held hostage by Ghazi.
Ghazi said he had nearly 2,000 followers with him and that no one was being held hostage.