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ISLAMABAD — The battle between Pakistan’s judiciary and government took a fresh twist Thursday when a court issued an arrest warrant for a close ally of President Asif Ali Zardari, effectively blocking the man’s nomination as the country’s next prime minister.

Zardari wanted Makhdoom Shahabuddin, a former health minister from Punjab Province, to replace Yousuf Raza Gilani, who was dismissed as prime minister by the Supreme Court on Wednesday.

But hours after Shahabuddin’s nomination, the military-run Anti-Narcotics Force prompted a court to order his arrest on charges relating to the illegal production of a controlled drug two years ago.

The court also issued an arrest warrant for Ali Musa Gilani, a son of the outgoing prime minister, in the same case.

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Hours later, Zardari’s Pakistan Peoples Party, which leads the governing coalition, had two new options for the post step forward: Qamar Zaman Kaira, the former information minister, and Raja Pervez Ashraf, a former minister for water and power.

The party said it would indicate its choice by midday Friday, ahead of an expected confirmation vote in Parliament that night.

The dramatic court maneuver highlights the growing difficulty of separating law from politics in the country’s rapidly evolving machinations of power.

Zardari’s supporters, and some analysts, say the judiciary is using its widening powers to erode the authority of the government and ultimately push it from power.

“Absolutely no subtlety anymore in going after the government. Amazing,’’ Nadeem F. Paracha, a newspaper columnist, wrote on Twitter.

The Supreme Court, led by Chief Justice Iftikhar Muhammad Chaudhry, insists it is standing its ground against an incompetent and corruption-riddled administration. At the same time, it has shrugged off corrosive graft accusations against Chaudhry’s son.

In the background, meanwhile, lies the country’s powerful generals, who also harbor deep animosity toward Zardari. With the arrests ordered in the drugs case, the generals, until now largely quiet in the political crisis, have entered the fray.

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The Anti-Narcotics Force, which has pursued the investigation that led to Shahabuddin’s arrest warrant Thursday, is headed by a two-star general. The warrant was obtained by the lead investigator, Brigadier Faheem Ahmed Khan, who is also a serving officer.

The antidrug force has said in court that Ali Musa Gilani used his father’s name to obtain the illegal production of 9,500 kilograms of ephedrine, a controlled drug used to manufacture methamphetamine, in 2010, at a time when Shahabuddin was health minister.

Ali Musa Gilani and Shahabuddin have rejected the charges, and their supporters say they are part of a wider power battle involving the ­judiciary, government and military.

Salman Raja, a lawyer for Ali Musa Gilani, said there was no substantial evidence against his client.

He accused the Anti-Narcotics Force of pressuring senior health ministry officials to testify against Ali Musa Gilani.

‘’They have been badgering and harassing people in the Ministry of Health, begging them to name him. It’s all very cynical and targeted. An absolute disgrace,’’ Raja said in a telephone interview.

It is not the only case that has tarnished the son of a leading public figure. Last week Pakistanis were riveted when Malik Riaz Hussain, a billionaire property developer with ties to both the military and Zardari’s political party, said he gave $3.7 million in kickbacks to Chaudhry’s son, Arsalan Iftikhar, in a bid to influence the outcome of several court cases.

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The scandal spread to the media when it emerged that two senior journalists had orchestrated a television interview with Hussain.

Yousuf Gilani was ousted this week because he refused court orders to reopen a dormant corruption inquiry into Zardari’s finances in Switzerland. Yousuf Gilani argued that as president, Zardari was immune from prosecution.

The next prime minister will probably quickly face the same order from the Supreme Court to investigate Zardari, meaning tensions will continue to roil the fragile political setup.

Relations between Washington and Islamabad are strained over a host of issues, including blocked war supply lines to ­Afghanistan and Pakistan’s links to the Afghan Taliban.

The Obama administration has tried to work with Pakistan to get it more aligned to its goals but has had little success.


Material from the Associated Press was used in this report.