The court said a panel of four high court judges would conclude its findings within a month.
The “memogate” scandal concerns a note allegedly sent from Pakistan’s political leadership to US Adm Mike Mullen, via a former ambassador.
President Asif Ali Zardari‘s aides deny any links with the document.
Pakistan’s civilian leaders were allegedly worried that the army was about to launch a coup after US forces killed Osama Bin Laden in Abbottabad in May.
They say any court inquiry into the affair would be unnecessary and politically motivated. The government argues that a parliamentary committee is already looking into memogate.
Correspondents say Friday’s ruling will put additional pressure on the government and could even lead to President Zardari’s fall from power if a link is established.
“I think that this is one of the darkest days in history for the judiciary,” said a lawyer for Pakistan’s former ambassador to the US, Husain Haqqani – who denies any role in the affair.
“I said in the Supreme Court too that this is a very disappointing judgement. This is a judgement that places national security above fundamental rights,” lawyer Asma Jahangir said.
He was addressing party supporters on the anniversary of Bhutto’s killing.
He pointed to a hearing the Supreme Court opened over the leaked memo as proof the court has been inconsistent.