Abdul Qadeer Khan, Pakistan's best-known nuclear scientist, shocked the nation on Wednesday, when he went on television and confessed to leaking nuclear secrets.
He said he took full responsibility for proliferating nuclear weapons to Iran, Libya and North Korea.
The nuclear National Command Authority, made up of the country's top military and civilian leaders, met after his confession and requested a pardon for Mr Khan from the cabinet.
His admission of guilt and plea for mercy is an attempt by the army to put the biggest global scandal on nuclear weapons proliferation behind them as swiftly as possible.
A trial, even held in camera, may implicate political and military leaders, which may destabilise President Pervez Musharraf's government.
Mr Khan's case raises questions about the Pakistani military
Opposition parties have threatened to mount street protests if Mr Khan goes on trial. Islamic fundamentalist and secular parties denounced General Musharraf for trying to make him a scapegoat whilst absolving the army of any responsibility.
However, Qazi Hussain Ahmed, leader of the Islamic fundamentalist Jamaat-e-Islami, again insisted that Mr Khan had told him he had never signed a confession during their meeting on Tuesday.
"I don't think people like Khan should be tried. He is a national hero. He has developed the nuclear programme," Mr Ahmed said.
The meeting between General Musharraf and Mr Khan - and the scientist's appearance on television - appeared to be carefully choreographed by the government.
Mr Musharraf, dressed in his camouflage military uniform, looked grim throughout the meeting and spoke through pursed lips. Mr Khan, dressed in a tan Kashmir wool jacket, appeared to be bending towards him in supplication.
Wednesday's events also seem to have been closely co-ordinated with Washington, which is deeply anxious not to destabilise Mr Musharraf, who has sided with the US in the war against terrorism.
Pakistani nuclear experts said that in exchange for not embarrassing Mr Musharraf, the US is now likely to insist that Pakistan allow some degree of international safeguards on its nuclear programme
"President Musharraf has assured us that Pakistan was not involved in any kind of proliferation and I am talking about the government of Pakistan," said White House spokesman Scott McClellan.
The international community still needs Pakistan's close co-operation in curbing the resurgent Taleban in Afghanistan and catching Osama Bin Laden and the remnants of al-Qaeda who are hiding out in the Pakistan-Afghanistan border region.
The US and Britain have also expended much diplomatic capital in persuading India and Pakistan to begin peace talks on Kashmir.
The first formal meeting between the two countries is due to start on 16 February.
Undue international pressure on Mr Musharraf or domestic agitation could jeopardise that meeting.
However Pakistani nuclear experts said that in exchange for not embarrassing Mr Musharraf, the US is now likely to insist that Pakistan allow some degree of international safeguards on its nuclear programme.
Khan is credited with giving Pakistan a nuclear deterrent
The US is also likely to ask for greater controls on Pakistan's stockpile of nuclear weapons and vetting of the 6,000 scientists who work for the nuclear programme.
Many of Pakistan's nuclear scientists are committed Islamic fundamentalists.
Such negotiations are likely to be carried in secret.
However, the fall-out of Pakistan's proliferation is likely to continue, with even greater international scrutiny on the nuclear programmes of North Korea and Iran, and the arrest of those middlemen in Europe, Africa and Dubai whom Khan has named. They allegedly helped him ship nuclear technology to these countries.