Troops are blocking all entrances and roads to the mosque
Ejaz-ul-Haq said the militants were "hardened terrorists" holding women and children hostage inside the Red Mosque.
The Pakistani army has kept a tight grip on the mosque, also known as Lal Masjid, since fighting began last week.
The mosque's leader, Abdul Rashid Ghazi, said he and his followers would commit suicide rather than surrender.
An army commander was shot dead by students inside the mosque on Sunday.
At least 21 people have been killed since the stand-off began last Tuesday.
Abdul Rashid Ghazi said as many as 1,800 followers remained in the mosque, although this cannot be verified.
'Al-Qaeda links'
Mr ul-Haq told the BBC that between two and five of the militants were wanted in connection with "high-profile cases".
Mr ul-Haq said the government became aware of the militants' presence after a man killed on the first day of the siege was identified as Maqsood Ahmed, a member of Jaish-e-Mohammad, an outlawed radical Muslim organisation which has been linked to al-Qaeda.
Ahmed was wanted in connection with an assassination attempt against Pakistani Prime Minister Shaukat Aziz in the northern Pakistani town of Attock in 2004.
Abdul Rashid Ghazi has denied the presence of any banned extremist groups. He says those inside are students of his religious school and he is in charge.
Earlier, Mr ul-Haq said up to 250 militants - including foreign radicals - were leading the fighting.
'Surrender or die'
Lt Col Haroon Islam, who died on Sunday, was in charge of an operation to blow holes in the mosque compound walls to enable civilians to escape.
Water and power to the mosque have been cut off and food is said to be getting scarce.
Our correspondent says he has heard intermittent gunfire in the area and the boom of heavy weapons.
Col Islam was shot dead by students inside the mosque
An increased military presence on the streets, combined with the refusal to let a delegation of Islamic figures through to the mosque, suggests that the government is now closing the door to negotiation, our correspondent adds.
On Saturday, Pakistani President Pervez Musharraf told the students they had no option but to surrender.
"We have been patient. I want to say to the ones who have been left inside: they should come out and surrender, and if they don't, I am saying this here and now: they will be killed," he said.
More than 1,000 supporters left last week under mounting pressure from security forces, although only about 20 have left since Friday.
Since last Tuesday, following violent confrontations with Pakistan's army, up to 1800 clerics and students are still holed up in Islamabad's Red Mosque. Clashes began last week following mounting antagonism between the mosques hard-line leaders and the government lead by President Pervez Musharraf. 

The mosque has been accused of enforcing its own Islamic law in the capital, notably the illegal detention of Chinese foreign nationals working in massage parlors.

20 people have been reported killed over the past six days, which have seen multiple gun battles and demolition of the mosques exterior walls. Currently, there seems little chance of a negotiated resolution. A delegation of Islamic leaders were refused access, and the mosques leader Abdul Rashid Ghazi has declared suicide a favourable option to surrender.

The mosques leaders follow the Hanafi school of thought, believing that the Koran is the authority by which justice should be metered. Historically the mosque has had close links with the Pakistan leadership, and members of the current administration have resisted calls for a crackdown on the mosques provocative behaviour.

The stand-off represents a decisive ideological challenge to the president who is walking a fine-line between Islamic extremists at home and foreign pressure to crack-down on militancy in the lawless tribal regions.