The refusal came on Thursday after Pakistani President Pervez Musharraf pardoned its top scientist Abd al-Qadir Khan for smuggling out nuclear technology to Iran, Libya and North Korea.
Soon after pardoning the scientist, Musharraf angrily rejected calls for an independent inquiry into the Pakistani military's role in the nuclear leaks, saying Pakistan would not hand over any documents or allow UN supervision of its atomic programme.
But shortly after, Pakistan's Foreign Minister Khursheed Mehmood Kasuri said there has been a "misunderstanding" and what the president meant was Pakistan would not allow the UN's nuclear watchdog to investigate Pakistan's own nuclear programmes, although it would help the body investigate Iran.
"What he said is actually that we are under no obligations," Kasuri said. "We will cooperate with the International Atomic Energy Agency."
"What is the International Atomic Energy Agency (IAEA)'s function?.. It's a body that has come into the picture because Iran has signed the additional protocol. They wish to investigate whether Iran's declaration is correct or not," the minister said.
"We will not allow them under any situation whatsoever to come and peep into our programme. These are our national secrets. But wherever they need support to achieve their declared objectives…we will fully cooperate," Kasuri explained.
Both Pakistan and arch-rival India have refused to sign the Non-Proliferation Treaty, designed to halt the acquisition of nuclear weapons capability to countries other than the five permanent members of the UN Security Council.
Khan admitted leaking nuclear
secrets and begged for pardon
Critics sniped that Pakistan had much to hide and its promise to cooperate fell way short.
Mohammad al-Baradai, head of the IAEA, said the pardoned Pakistani scientist had help from people in many countries and was "the tip of an iceberg."
Many Western diplomats also doubted Khan could have acted independently of Pakistan's military, which controls the nuclear arsenal, and said he had been used as a scapegoat for the army.
Khan, considered the father of Pakistan's atomic bomb and a national hero, had been under investigation together with other scientists for leaking nuclear secrets to Iran, Libya and North Korea.
He finally admitted his wrongdoing and pleaded for clemency in a televised speech on Wednesday.
In pardoning him, Musharraf said Khan still remained a national hero.