Mrs Bhutto’s allies have rubbished the claim but, if true, his revelations raises fresh questions about Pakistan’s role in the spread of nuclear weapons and brings the threat of sanctions.
Dr Khan is known as the father of Pakistan’s atom bomb but was also at the centre of a proliferation network that sold secret technology to rogue states around the world, including Libya and Iran.
In 2004 he signed a confession claiming that he acted without the consent of the government and was pardoned the following day, an account he has now contradicted.
“The then Prime Minister Benazir Bhutto summoned me and named the two countries which were to be assisted,” Dr Khan said in an interview with the Jang media group, without naming the two nations.
He said he had no option but to obey Mrs Bhutto, who was prime minister from 1988 until 1990 and 1993 to 1996. She died in a suicide attack in 2007.
“The Prime Minister would have certainly known about the role and co-operation of the two countries, mentioned by her, in our national interest,” he claimed, adding that the transfer of nuclear technology was a complex procedure which needed the help of hundreds of people.
He declined to discuss the issue with The Daily Telegraph or explain Mrs Bhutto’s motivation and when their conversation took place.
Dr Khan, 76, who was released from house arrest in 2009, remains a national hero for his role in helping develop a nuclear warhead, which was successfully tested in May 1998 – the first in the Islamic World.
The US has repeatedly asked to question him about his role in selling nuclear secrets but has been rebuffed.
He has admitted supplying centrifuge technology to Iran, North Korea and Libya, in return for cash.
He is also suspected of offering secrets to Iraq, as part of a covert operation that ran for about 10 years until 1999.
Members of Mrs Bhutto’s political party and government officials all denied that she – or her government – was involved in nuclear proliferation and criticized Dr Khan for making allegations against a woman who could not defend herself.