But in his latest interview, Khan said the army had "complete knowledge" of the shipment of used P-1 centrifuges to North Korea and that it must have been sent with the consent of Musharraf, the then-army chief and who seized power in 1999.
"It was a North Korean plane, and the army had complete knowledge about it and the equipment," Khan said. "It must have gone with his [Musharraf's] consent."
Khan's allegations, reported earlier on Friday by Kyodo, the Japanese news agency, are his most controversial yet and could prove deeply embarrassing for both the army and Musharraf, a key ally in the US-led war on terror.
Rashid Qureshi, Musharraf's spokesman, rejected Khan's claims.
"I can say with full confidence that it is all lies and false statements," he said.
Army and foreign ministry spokesmen declined to give immediate comment.
Khan is regarded as a hero by many in Pakistan for his key role in the programme that developed the country's nuclear bomb in 1998, following several tests by rival India of its own nuclear weaponary.
After his 2004 confession and televised statement of contrition, Khan was pardoned by Musharraf but has been kept under virtual house arrest at his spacious villa in Islamabad.
Since a new civilian government took power after February elections, eclipsing Musharraf, the retired scientist has increasingly spoken out in the media.
Asked why he had taken sole responsibility for the nuclear proliferation, Khan said he had been persuaded that it was in the national interest by friends including Chaudhry Shujaat Hussain, a key figure in the-then ruling party.
Khan said that in return he had been promised complete freedom, but "those promises were not honored".