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 government to ensure that Haqqani is brought back to Pakistan in four weeks.
If Haqqani does not appear in court, the government can proceed with the trial, said Justice Asif Khosa.
The memo allegedly committed Pakistan to wide-ranging changes in its national security set-up, including the removal of military officials believed to have links to militants.
Haqqani has denied the allegations and is currently in the US. He has said he will not come to Pakistan for the hearing of the case because of serious threats to his life.
His lawyer Asma Jahangir told the bench during today's proceedings that her client continued to have security concerns.
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 the government to adopt all constitutional and legal procedures to facilitate Haqqani's appearance in court.
He further said Haqqani is not an accused and the Constitution protects the fundamental rights of all citizens.
The apex court subsequently adjourned the case for four weeks.
