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Pakistan Sunni Muslim cleric Tahir-ul-Qadri addresses his supporters behind a bullet-proof glass at an anti-government rally in Islamabad, Pakistan, Tuesday, Jan. 15, 2013. Thousands of anti-government protesters are rallying in the streets of Pakistani capital for second day despite early-morning clashed with police who fired off shots and tear gas to disperse the crown.

Muhammed Muheisen/AP

The government of Pakistan was plunged into crisis Tuesday as it faced simultaneous challenges to its authority, with followers of a Toronto-area cleric clashing with riot police and the country's highest court ordering the arrest of Prime Minister Raja Pervez Ashraf and 15 others on corruption allegations.

Tuesday's court order came as an estimated 30,000 protesters, led by Muhammad Tahir-ul-Qadri, a cleric who only last month lived in Canada, camped out in Islamabad for a second night and also rallied against corruption, promising not to leave until the government bars venal politicians from seeking office and instead allows the army to shape a caretaker government ahead of federal elections expected in May.

"We are here in front of the parliament house just to save our country from collapse and from complete ruin," Mr. Qadri said in his address, delivered from behind bulletproof glass. "We want to put democracy in its letter and spirit in place."

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Mr. Qadri also supported the call by the country's Supreme Court for the arrest of Mr. Ashraf, who is accused of allegedly receiving bribes while he was federal minister for water and power. He became Prime Minister after Yousaf Raza Gilani was forced to quit in June, 2012.

For Pakistan's Western allies, the political upheaval raises worries that the strife will destabilize the nuclear power, just as it faces domestic Islamic militancy, rising tension with India and volatility in neighbouring Afghanistan.

The coincidence of the two crises raises questions about the timing of the arrest order issued by the Supreme Court and Chief Justice Iftikhar Chaudhry, a magistrate with a history of hostility against the current administration.

If the government of the Pakistan Peoples Party (PPP) survives these crises and completes a full term – it came to power in democratic elections in 2008 – it would be a first for any party in a country where the democratic process has often been derailed by the army, the country's most powerful institution.

In the past, Mr. Chaudhry has pursued corruption cases against President Asif Ali Zardari, the husband of slain PPP leader Benazir Bhutto.

Last year, Mr. Chaudhry barred Mr. Gilani from his position of prime minister after Mr. Gilani would not follow through on the court's order to investigate corruption charges against Mr. Zardari. The President's allies argued that the two-decades-old charges were politically motivated. The ruling barring Mr. Gilani paved the way for Mr. Ashraf.

"When it comes to the PPP, I don't think there's any question that this justice is operating purely out of vendetta. Because if this were all about corruption, there are equally corrupt people in all of the parties, for crying out loud – including the Islamist parties," said C. Christine Fair, an assistant professor at the Center for Peace and Security Studies at Georgetown University.

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The grudge between the chief justice and the President goes back to the beginning of the current civilian government, when Mr. Chaudhry's allies perceived the PPP government to be blocking his reappointment after he was fired during the regime of General Pervez Musharraf.

The arrival of Mr. Qadri, who led a caravan of vehicles from the eastern city of Lahore to the capital, was "another opportunity to hammer" the ruling party by the country's chief justice, says Ms. Fair, an expert in Pakistani affairs.

The timing of the mass protest and the chief justice's order against the Prime Minister has raised suspicions among many Pakistanis about who is financing Mr. Qadri's protest.

"Think about the fact that just the food bill – forget about transportation, forget all the advertising that's been invested – just the food bill comes to a quarter-million dollars. So where's this money coming from?" said Mosharraf Zaidi, a Canadian-raised Pakistani political commentator who is a former foreign policy adviser to the current civilian government.

"For some people the immediate answer is the military. I think that's become a bit of a Pakistani habit that we immediately suspect the military of being involved in these things," he said, adding that people are somewhat justified in their suspicion given the long history of military rule.

But, even as it is hobbled by the latest challenges, Pakistan will likely continue its transition to stable civilian rule, analysts say.

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"There will be a lot of upheaval on the way there, but I think we will have [free and fair] elections," Mr. Zaidi said.

Ms. Fair said: "They [Pakistan] never really seem to go sinking to the bottom, as all the naysayers say. I'm actually fairly confident that this election will go forward and we are going to see this important transition."

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