He said it was his fundamental right to come to the court.
Ahmar Bilal Soofi, appearing on behalf of the federation, contended that there could be complications if Dr Qadeer came to the court.
He said it would be better if this case is heard in the chamber.
Justice Mushir Alam remarked that they don't have to ask Dr Qadeer how a bomb is made. "There is no reason to hear this case in the chamber," he added. Justice Afridi said they acknowledged Dr Qadeer's contribution for Pakistan.
He said the Islamabad High Court (IHC) in 2009 had passed the judgment regarding the matter with the consent of both the parties, adding the IHC decision was not challenged in the last 10 years.
Justice Afridi said after 10 years Dr Abdul Qadeer filed another petition in the Lahore High Court (LHC).
He questioned how the Supreme Court could intervene in this matter now.
He asked Dr Qadeer's counsel to convince the court why he had not approached the IHC again.
Taufiq Asif said in the petition he has explained the reasons in detail for not going to Islamabad High Court (IHC).
The counsel said that he also explained in detail how an affidavit was "obtained" from Dr Qadeer.
He said in matters of citizens' fundamental rights the apex court can directly intervene, adding being a Pakistani citizen Dr Abdul Qadeer also has such rights.
Justice Mushir remarked it was the responsibility of the lawyers not to humiliate a 'national hero'.
Justice Yahya stated why Dr Qadeer wasted time and did not approach a proper forum.
The judge asked Dr Qadeer's lawyer to inform the court after consulting his client. Taufiq Asif said on Tuesday again Dr Qadeer was not allowed to come to the court. The nuclear scientist is also not permitted to freely meet his counsel. The case was adjourned for today (Wednesday).