Maj. Gen. Athar Abbas said an article written by a UK-based security expert was false because none of the bases named actually had any nuclear facilities.
'It is factually incorrect,' he said.
Taliban militants brief takeover of areas some 60 miles from the capital, Islamabad, raised new fears about the security of Pakistans atomic weapons being seized by extremists linked to al-Qaeda, although the country insists its arsenal is secure.
Shaun Gregory, a professor at Bradford Universitys Pakistan Security Research Unit, wrote that several militant attacks have already hit military bases where nuclear components are secretly stored. The article appeared in the July newsletter of the Combating Terrorism Center of the US Military Academy at West Point.
The most recent assault, he wrote, was the August 2008 coordinated suicide bombings of the Wah Cantonment ordnance factory, which he said is considered one of Pakistans main nuclear weapons assembly sites.
The other two attacks were in late 2007 on the Sargodha air base, which Gregory identified as a nuclear missile storage facility and the nuclear air base at Kamra, the article said.
While all three suicide attacks appeared aimed at causing maximum carnage and not seizing weapons, Gregory said they highlighted the vulnerability of the nuclear storage facilities to assault.
'The risk of the transfer of nuclear weapons, weapons components or nuclear expertise to terrorists in Pakistan is genuine.'
Abbas said Wednesday that none of the military bases named were used to store atomic weapons. He said the Wah ordnance factory makes small arms ammunition, Kamra is an air force facility and Sargodha is an air force ammunition dump for conventional weapons.
'These are nowhere close to any nuclear facility,' he said.
He added that the Pentagon has recently expressed faith in Pakistans security measures, which among other things keep weapons components and triggering devices separate.
Khalid Kidwai, head of the Strategic Plans Division which handles Pakistans nuclear arsenal, told journalists last year that Pakistan uses 10,000 soldiers to keep the weapons safe and has received up to $10 million in US assistance to enhance security.
'We are very confident that the security standards that we are following are world-standard,' Abbas said. 'There is absolutely no chance of them falling into the hands of any extremists or terrorists.'