Abdul Qadeer Khan, founder of the nuclear programme confessed on Wednesday in a televised statement that he leaked nuclear technology overseas during 25 years at the helm of Khan Research Laboratories (KRL).
Khan, who appears set to receive clemency after cabinet recommended a presidential pardon on Thursday, said that the leaks during the past two decades were not authorised by any government or official.
Investigators earlier said Khan had shared sensitive nuclear technology with Iran, Libya and North Korea for more than a decade.
Khan took "full responsibility" for the proliferation and said his subordinates who have confessed to proliferating nuclear technology had only followed his instructions.
But Mohamed ElBaradei, the head of the watchdog International Atomic Energy Agency, said Thursday Khan was "the tip of the iceberg", with analysts in Pakistan agreeing the question of state involvement remained unanswered.
"The issue of the state responsibility or institutional responsibility regarding the nuclear leaks remain wide open," Riffat Hussain, head of the strategic studies department at Islamabad's Quaid-e-Azam University told AFP.
"Even though A.Q. Khan has admitted there was no explicit government permission given to him, still it really strains the credibility to argue that he could have done all this without the tacit approval of those who were supposed to have kept a watch on him," Hussain said.
Analyst Hasan Askari said the international community would continue to doubt Khan's confession that he was the only one responsible for the proliferation.
"Despite the confession of Dr. A.Q. Khan the international community would continue to doubt the credibility of the confession to the extent that he was the only person responsible for it," Askari, former head of the political science department at the Punjab university, told AFP.
"The security system of the nuclear installations is so tight that one wonders how could things move out without the knowledge and information of the security agencies.
"So the government will have to do this kind of explaining."
Hussain said Khan's carefully scripted confession had been designed to lay the matter to rest once and for all, snuffing out the possibility of a trial and the risk of damaging revelations emerging.
"(It was) quite obvious that a deal was cut to close the issue and not let it develop into a confrontation with unpredictable consequences," Hussain said.
Analyst Najam Sethi said it was hard to believe that Dr. Khan could have proliferated on his own without the knowledge of the government.
"Most Pakistanis don't believe that the scientist could have proliferated to such an extent without the knowledge of and in some cases approval of the government officials incharge of the programme," Sethi said.
The cabinet at a special meeting here Thursday recommended that the president pardon Khan following his confession, officials said.
Khan offered his "deepest regrets" and "unqualified apologies" to the nation for his involvement in "unauthorized" proliferation activities."
The president consulted the National Command Authority which decided to forward the clemency appeal to the cabinet for final decision.