The top court also said that the panel would decide on controversial Pakistani-American businessman Mansoor Ijaz's request to record his statement outside the country.
A nine-judge bench headed by Chief Justice Iftikhar Chaudhry lifted a foreign travel ban on Haqqani, who had resigned over the scandal in November.
Acting on an application filed by the three-judge commission seeking an extension of its term, the bench gave the panel two more months to complete its probe.
Attorney General Anwar-ul-Haq told the bench that the government did not have any reservations on term of the commission being extended.
The Supreme Court had formed the commission on December 30 and given it four weeks to complete its investigation.
The term of the commission would have ended today.
The apex court rejected an application from Ijaz that said the commission should be asked to record his statement outside Pakistan. The court said the commission should decide whether it wants to go abroad to record Ijaz's statement or to call him to Pakistan.
Acting on a request from Haqqani's counsel Asma Jehangir to ease travel restrictions on her client who had family abroad, the Supreme Court ended a ban on foreign travel it had imposed on the former envoy. However, the bench said that whenever the judicial commission or the apex court summoned Haqqani, he would have to come back to Pakistan in four days.
The bench further directed Haqqani to inform the apex court's registrar's office whenever he travelled abroad.
Haqqani, who has denied any involvement in the memo, said he plans to travel to the US to join his family there.
Ijaz, who made the mysterious memo public, has failed to make two scheduled appearances before the commission, which has given him a final opportunity to depose on February 9.
The Attorney General further informed the bench that Canadian firm Research In Motion had refused to hand over data of alleged conversations between Ijaz and Haqqani.
RIM had said it would consider the request to hand over this data if the Canadian government writes an application and Ijaz gave a waiver regarding the handing over of data regarding his communications, the Attorney General said.
Reacting to top court lifting his travel ban, Haqqani in messages posted on Twitter wrote that the Supreme Court had restored his freedom to travel.
"Lest (someone) forgets, I returned and resigned voluntarily to disprove falsehoods," he wrote.
Haqqani wrote that he and his counsel would continue to cooperate with the commission.
"So far I'm the (only one to) appear before it," he said.
Acting on a batch of petitions, the apex court last year formed the commission to probe the alleged memo that had sought US help to stave off a feared military takeover in Pakistan after the killing of Osama bin Laden.
The scandal triggered a standoff between the civilian government and the powerful military, which urged the apex court to order an investigation.
The government insisted that the probe should be handled by the Parliamentary Committee on National Security, which too has summoned Ijaz to appear before it on February 10