The order was issued by a nine-judge larger bench headed by Chief Justice Iftikhar Chaudhry, which is hearing several petitions on the "Memogate" issue, including one filed by Prime Minister-designate Nawaz Sharif.
The apex court directed the Interior and Foreign Secretaries to take steps to bring Haqqani back to Pakistan in four weeks.
The bench further directed the Attorney General and the secretaries to ensure a foolproof security plan for Haqqani.
His lawyer Asma Jahangir told the bench during today's proceedings that she had spoken with her client last night and he was not ready to return to Pakistan because of security concerns.
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The Chief Justice remarked that the court has the option to try Haqqani in his absence if he does not come back.
Justice Asif Khosa remarked the trial could be initiated against Haqqani without his presence.
Haqqani was accused of delivering to the US military a secret memorandum that allegedly sought help to prevent a coup in Pakistan in the wake of the American raid that killed Osama bin Laden in May 2011.
Haqqani has denied the allegations.
Jahangir said Haqqani feared the trial would not be free and fair as Sharif, who is one of the petitioners, is set to become premier within a few days.
The Chief Justice remarked that it makes no difference who becomes the Prime Minister as the issue will be decided according to the law.
No one will be allowed to exploit any one, he said.
The Chief Justice directed authorities to adopt all constitutional and legal procedures to facilitate Haqqani's appearance in court.
The court subsequently adjourned the case for four weeks.