Gilani has been summoned to appear before the court on January 19.
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The graft cases date back to the 1990s and concern the country's president, Asif Ali Zardari, along with other officials.
Speaking outside the court, in Islamabad, Pakistani Law Minister Moula Bakhsh Chandio told journalists the decision was “not a small, usual thing," Reuters reported:
"This is a Supreme Court order on which we will consult our committee of experts. We will take the necessary steps in light of the constitution and the law."
The court order, which raises the prospect of Gilani's prosecution, increases pressure on Pakistan's civilian government, amid a row between the PPP leadership and the country's army.
Last week, the army warned of "potential grievous consequences” after Gilani sacked his defense secretary, who was considered close to the generals, AFP reported.
It is understood that a key vote of confidence in Pakistan's government is to be put to the parliament.
Separately, a commission that was today appointed by the court resumed hearings into the "Memogate" scandal – concerning a secret memorandum allegedly written by Pakistan's former ambassador to the United States, the BBC reported.
In the memo, the US was allegedly asked for help in thwarting a possible military coup after al-Qaeda leader Osama bin Laden was killed in a US raid on Pakistani territory.
Update: AFP also report that Gilani said he would comply with the summons.
"The court has summoned me and I will appear before it as a mark of respect on January 19," he said in an address televised by Pakistani TV channels.
"There can be difference of opinion with the judiciary and the military but they cannot either pack up or derail the whole system. Rather, they have to strengthen it."