An anti-narcotics court judge in the northern city of Rawalpindi has issued an arrest warrant for the candidate nominated for the prime minister's post by President Asif Ali Zardari.
The judge on Thursday cited Makhdoom Shahabuddin's alleged role in a scandal involving the import of a drug that can be used to make methamphetamine.
Shahabuddin, a member of the ruling Pakistan People's Party (PPP), filed his nomination papers on Thursday. Two other PPP leaders, Raja Pervez Ashraf and Qamar Zaman Kaira, also filed their nomination papers as alternative candidates.
Asked about the reported arrest warrant after he filed his papers, Shahabuddin said he was not afraid of "hostile winds".
It is unclear whether the development could derail his nomination. Legal cases are routinely filed against Pakistani politicians by rivals as a means of weakening them. Often, the cases drag on in the courts for years, and the politician's career is unhindered.
Shahabuddin was health minister when the scandal broke, to which Gilani's son has also been linked.
It revolves around two Pakistani pharmaceutical companies that allegedly used political connections to obtain huge amounts of ephedrine in 2010. They are suspected of diverting it to people in the drug trade who could have used it to make methamphetamines worth billions of dollars.
The companies have denied any wrongdoing, as has Gilani's son.
Shahabuddin, 65, comes from a wealthy, landowning family based in the central Pakistani district of Rahim Yar Khan. His father had served as minister in the cabinets of two Pakistani governments. He also served as minister for finance and health in the current government.
Although the ruling PPP coalition has a majority in the house, Shahabuddin will face opposition from the Pakistan Muslim League-N nominee when the national assembly meets on Friday to elect the new premier.
"The opposition will be fielding its candidate, Mehtab Khan Abbasi, but Shahabuddin is likely to be the next prime minister," Al Jazeera's Kamal Hyder, reporting from Islamabad, said.
He said the opposition has made attempts to woe PPP members disgruntled by Shahabuddin's appointment.
Early polls likely
The PPP said it "accepted" a Supreme Court order on Tuesday that Gilani could not remain in his post.
Gilani, the nation's first-ever sitting prime minister to be convicted, can have the verdict reviewed, but has no formal appeal process available to him.
The PPP is the largest party in parliament but does not have a majority, so its coalition partners will insist on concessions for their support for a new premier and the process may not be smooth.
Whoever takes over will not have long in power as the government must call elections before March next year.
Under the constitution, polls can only be held under a caretaker government, which must be in place three months before election day.
Many analysts have speculated that the current political upheaval may expedite the polls, possibly in November.
The new prime minister will also likely run into trouble with the supreme court, which is likely to make the same demand of him, or her, as it did of Gilani, to initiate a corruption probe against Zardari.
The court has been criticised by some for taking political decisions and jeopardising the democratic set-up in Pakistan.