It says that the release of a key suspect linked to Dr Khan's network means that the inquiry into his operations has come to a close. A former national hero, he has been under virtual house arrest since February 2004. In 2004 he admitted leaking nuclear secrets to North Korea, Libya and Iran.
A military spokesman said that Dr Mohammed Farooq was released from custody a few days ago and had been told not to leave his residence in Islamabad.
Dr Farooq worked at Pakistan's premier nuclear weapons facility, Khan Research Laboratories (KRL), and was detained in December 2003 along with 10 others.
Pakistani Foreign Ministry spokesperson Tasnim Aslam said that inquiries into Dr Khan's proliferation network began more than two years ago.
She said the investigation into the sale of nuclear information and material to other countries had been "thorough".
Responding to questions, Ms Aslam said that the International Atomic Energy Agency (IAEA) and key countries including the US had been kept informed of the progress of the investigation during the entire process.
She said that both the IAEA and the US were fully satisfied with Pakistan's handling of the issue.
However, she said at no stage were officials and organisations - including those from concerned countries - allowed direct access to Dr Khan.
Ms Aslam confirmed that Dr Farooq was the last of Dr Khan's team members to be freed from detention.
And on a specific question about the state of investigations, the foreign office spokesperson said that it could be "presumed" that Dr Farooq's release meant that the investigations would be drawn to a close.
Dr Khan is regarded in Pakistan as the father of the country's nuclear weapons programme.
President Musharraf pardoned him because of his status in the country as a national hero, although the allegation against him and others working in his proliferation network was that they secretly sold bomb designs and centrifuges during the 1990s.
It is not clear whether Mohammed Farooq was found guilty of any wrongdoing.
But even after being allowed to return to his family, he has been specifically instructed to remain indoors, and not to communicate with the media.
Most people in Islamabad are convinced that like Dr Khan, he is under virtual house-arrest.Güncelleme Tarihi: 20 Eylül 2018, 18:16