The US Secretary of State Colin Powell has demanded that Pakistan dismantle "by its roots" the secret network of nuclear technology deals.
Khan is widely seen in Pakistan as a hero for his nuclear work
Mr Powell said that Pakistan had already done "quite a bit" to roll up the proliferation network.
Islamabad has already announced that the disgraced nuclear scientist Abdul Qadeer Khan may face more questions.
The government has also said it will share the findings of an inquiry into the leaks with the UN.
Mr Powell said he had urged President Pervez Musharraf to make sure that no more of the secret nuclear exchange network of Dr Abdul Qadeer Khan remained.
The US secretary of state said he had received assurances that the Pakistani government shared his objective, and that Islamabad would share all the information it came up with.
The Pakistan government has already announced that it is prepared to share the findings of an investigation into the secret transfers with the UN's International Atomic Energy Agency.
Islamabad has repeatedly stressed that it wants to eliminate the world black market in nuclear-related material.
Correspondents say that because General Musharraf is a close ally of the US, its response so far to the leaking of Pakistani nuclear secrets has been muted.
But at the same time the US has made no secret of its determination to investigate and stop the spread of technology and weapons.
Pakistan earlier said that Dr Khan had not been granted a "blanket pardon" and may face further questioning.
The government said an investigation into his leaking of nuclear secrets to other states was continuing.
But officials also stress that Pakistan's nuclear arsenal is not in danger of falling into the hands of extremists.
Foreign ministry spokesman Masood Khan said that the pardon given to Dr Khan was "conditional" and applied only to his confession made so far.
He refused to say whether the case against the scientist could re-open if more incriminating evidence was found against him.
Last week General Musharraf described Dr Khan as a "national hero" for his role in developing Pakistani nuclear weapons technology.
Khan's confession shocked the nation
The president granted a pardon after Dr Khan went on television and begged the nation's forgiveness for passing on information to Iran, Libya and North Korea.
Masood Khan said the scientist had been co-operating with the authorities in the investigations and that his pardon was subject to his continued co-operation.
He described allegations that there was nuclear technology on board a Pakistani C-130 cargo aircraft flight to North Korea in July 2002 as "utter nonsense".
He said that while the flight had taken place it was only to allow Pakistan to pick up shoulder-fired anti-aircraft missiles.
The spokesman described the revelations about the involvement of Pakistan's top scientist in proliferation as a traumatic experience for the country and its citizens.
But he said it was a necessary exercise and the people had to go through this pain in order to convince the world that only a few individuals - and not the whole country - was involved in proliferation.
Strict security restrictions have been imposed on Dr Khan and his associates.
The government says they will not be allowed to resume their normal duties or activities.
Relatives of six scientists detained in relation to the nuclear scandal have taken the government to court to challenge the legality of their continued imprisonment.