The base was in a madrassa, or Islamic school, and a nearby compound owned by the son of a former minister of the Taliban government that ruled Afghanistan until late 2001, Lieutenant General Safdar Hussain said in the city of Peshawar.
He said the owner, Sirajuddin Haqqani, whom he described as a senior Al-Qaida insurgent, had escaped after a tip off.
Hussain said an official who tipped off Haqqani and allowed him to escape had been arrested.
"The raid on the Haqqani madrassa and compound is still going on but we can say we have busted the biggest al-Qaida terrorist den in North Waziristan," Hussain, who commands troops in northwestern Pakistan, told reporters on Thursday.
"We have recovered 15 truckloads of ammunition and weapons from there and arms and ammunition are still being recovered," he said.
"We also busted a communications centre which was used to coordinate operations in Afghanistan."
Rebels loyal to the Taliban and its ally al-Qaida are suspected of crossing from bases in Pakistan to Afghanistan to launch attacks.
Seven rebels were captured in the operation, raising the number arrested this week to 28, Major General Mohammad Akram Sahi said in the nearby border town of Miranshah where journalists were shown another cache of weapons recovered from militant hideouts.
"All 28 are Afghans," Sahi told reporters.
The weapons found in 18 compounds in the Miranshah area included anti-aircraft guns, rockets, improvised explosive devices, communication equipment and military fatigues.
Troops said they found 15
truckloads of weapons
Among them were pictures of Sirajuddin Haqqani and his father Jalaluddin Haqqani, a former anti-Soviet fighter who later served as the Taliban's minister for frontier regions.
Hussain, in Peshawar, said the border between the countries had been sealed and 763 guard posts had been established on the Pakistani side.
An overnight curfew had also been imposed and troops given orders to shoot on sight anyone found within five kilometres of the border, Hussain said.
However Afghanistan had only set up 120 posts on the border, he said. "They need to do more to stop infiltration," he said.
The operation would help to reduce bloodshed blamed on Taliban rebels in the run up to Afghanistan's parliamentary elections on Sunday, the general said.
Thousands of troops have swept
through the region
"Naturally it will reduce violence in Afghanistan," he said.
Pakistan would also conduct "extensive air surveillance with helicopters" on the day of the election, he said.
Pakistan pushed tens of thousands of troops into the tribal regions early last year to crack down on al-Qaida and Taliban rebels who fled there after the Taliban government was ousted by US-led forces after the September 2001 attacks on New York and Washington.
Pakistan said last week it was sending 9500 more troops to the border before the elections, bringing the total to 80,000.
Hussain said Pakistani forces had killed 353 rebels in the tribal areas since March 2004, including 175 foreigners such as Uzbeks, Tajiks, Turkmens, Chechens and a few Arabs.
Nearly 270 Pakistani troops have also died and more than 670 have been wounded, some losing limbs.