Abdul Qadeer Khan, the father of Pakistan's nuclear program, named ex-army chiefs Aslam Beg and Jehangir Karamat in an 11-page statement confessing to selling nuclear secrets to the three states between 1988 and 1997, the official said.
"He named two gentlemen, generals Beg and Karamat, who were then questioned," the military official told AFP on condition of anonymity.
"(Khan) said they were in the know. In one case he said he did it on their instructions, but not directly. They asked someone else and that fellow instructed A.Q. Khan and that man is now dead."
The middleman was the late brigadier Imtiaz Ali, defence adviser to Benazir Bhutto during her first tenure as prime minister from 1988 to 1990.
Both Beg, who was army chief from 1988 to 1991, and Karamat, army chief from 1997 to 1998, were "thoroughly" questioned during a two month probe by Pakistani investigators.
"There was no evidence found of what A.Q. Khan was saying, so it could not be sustained," the official said.
"If there is any more evidence of involvement of anyone else they will be questioned, no one is above the law."
Beg denied in interviews last week approving or being aware of the sale of nuclear secrets.
Khan himself, who is under virtual house arrest in his heavily-secured Islamabad home, has not been able to speak publicly.
President Pervez Musharraf, who has been army chief since 1998, has categorically denied any military knowledge or approval of the nuclear leaks, and has blamed civilian scientists and international black marketeers.
More than a dozen nuclear scientists, engineers and administrators have been questioned during the probe, which was prompted by information from Iran via the International Atomic Energy Agency (IAEA) in November.
Around half have been cleared and the probe narrowed last week to three ex-military officers and three nuclear scientists.
Apart from Khan, four others have confessed to transferring nuclear expertise but they have yet to be named, an official close to the investigation told AFP.