Khan "has accepted full responsibility for all the nuclear proliferation activities which were conducted by him during the period in which he was at the helm of affairs of the Khan Research Laboratories," the statement said on Wednesday.
Khan also "submitted his mercy petition to the president and requested for clemency", it added.
Musharraf was to consult the National Command Authority, the top decision-making body on Pakistan's nuclear and missile programme, before deciding whether to accept Khan's plea for mercy, the statement said.
State-run Pakistan television showed an interview with Khan who said he had told the president "what had happened".
"I gave him (Musharraf) the background what was happening and what had happened. He appreciated the frankness with which I gave him the details... and he will take a decision how to proceed and close this matter"
Abd al-Qadir Khan
"I gave him the background what was happening and what had happened," Khan told PTV.
"He (Musharraf) appreciated the frankness with which I gave him the details and he will discuss with the cabinet, with the prime minister, with other colleagues and then he will take a decision how to proceed and close this matter."
Khan seeks 'deal'
The statement quoted Khan as saying he "realised that these activities, which were in clear violation of different Pakistani
laws, could have seriously jeopardised Pakistan's nuclear capability and put the nation at risk".
Musharraf said the entire nation had been "severely traumatised by the unfortunate events in the last months," a reference to the investigation into nuclear leaks by Pakistani scientists to Iran, Libya and North Korea.
Intelligence sources said Khan had called the meeting with Musharraf in an attempt to strike a deal and avoid prosecution.
Many Pakistanis and western diplomats feel Khan has been treated as a scapegoat, and he could not have acted as he did without the knowledge of senior military officials.
Pakistan's military has denied remarks attributed to a friend of Khan saying the scientist had told investigators Musharraf was among those who knew he had given nuclear know-how to North Korea in the 1990s.