Pakistan is facing a deepening crisis after the country’s highest court ordered the arrest of the Prime Minister today, just hours after tens of thousands of protesters demanding the dismissal of the government engulfed the capital.

In scenes that many believe represented little short of an unfolding coup, the Supreme Court ordered the arrest of Raja Pervez Ashraf over allegations of corruption as up to 50,000 supporters of the charismatic Muslim cleric, Tahir ul-Qadri, staged a peaceful but debilitating sit-in in the heart of Islamabad.

Fawad Chaudhry, a special adviser to Mr Ashraf, claimed last night that the judiciary and the army were working in concert against the government to install an administration of its choosing. “This is the establishment working,” said Mr Chaudhry. “They want to dismiss the government and put in a long-term interim set-up.”

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Islamabad was paralysed after Dr Qadri, who had been living in Canada until his return to Pakistan last month, arrived with his followers on Monday night, occupying the city’s main thoroughfare. Defying the government’s orders, he told the crowd to move close to parliament, pushing aside the barricades erected by police. Dr Qadri has instructed the protesters to stay in the capital until his demands are met.

The five-year term of the current government, led by President Asif Ali Zardari, is due to end in the middle of March, at which point new elections would be overseen by an interim caretaker administration that is supposed to be neutral.

But Dr Qadri is demanding that the army have a say in the composition of the interim administration and that the caretaker government cleanse the political system to disbar most of the current “criminal” politicians.

“We are here just to save our country from collapse and complete ruin,” Dr Qadri told the crowd. “Ninety-nine per cent of the people have been kicked out of democracy. This democracy is only for the one per cent elite.”

While all of Pakistan’s governments have been criticised for corruption and misrule, critics say that Mr Zardari’s tenure has taken graft to new heights, while failing to tackle basic problems, including terrorism and an acute shortage of gas and electricity.

The Supreme Court has repeatedly gone after Mr Zardari, but so far he has been shielded by the constitutional immunity that the President enjoys.

Just as Dr Qadri was firing up the crowd in Islamabad, word came through that the Supreme Court had ordered the arrest of Prime Minister Ashraf and other officials “without hesitation” over a case that dates back to alleged kick-backs received while he was Minister for Power. Mr Ashraf himself came to power last year after the Supreme Court disqualified his predecessor, Yousuf Raza Gilani, for refusing to pursue old corruption charges against President Zardari.

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Dr Qadri and the crowd appeared to take the news not only as vindication, but almost as a divine intervention on their side. People knelt in prayer, embraced each other, tears in their eyes. “Half our job is done. We’ll do the other half tomorrow,” the cleric boomed over the loudspeakers. “Victory, victory.”

In the crowd, Farooq Hameed Khan, a retired army officer, said: “This government has lost the moral, legal and constitutional authority to rule this country. There is no point prolonging the agony of the people of Pakistan any longer.”

It remains unclear whether the court’s arrest order will be implemented and by whom, with the police coming under an interior ministry that is run by a loyalist of the ruling Pakistan Peoples Party.

The army has denied persistent accusations that it is backing Dr Qadri, while links between him, the judiciary and the military are not proven. But Ayaz Amir, a member of parliament for the main opposition party, said that the fact that the army had not stopped the protesters from entering Islamabad showed that it had already chosen sides. The army maintains a special brigade which can be deployed to quell trouble in Islamabad – or stage coups.

“The countdown has started. The government is finished. It is dissolving bit by bit,” said Mr Amir, pointing to the protesters. “If there was a government existing here, they would have been able to disperse the crowd.”

Democracy remains fragile in Pakistan. The elections due this year – if they take place – would be the first time that an elected government completes its term and hands over to another elected government.

Ali Dayan Hasan, Pakistan director for Human Rights Watch, said that it would be “extremely naïve” to believe that the court order was coincidental to the protest.

“What is being created is a constitutional crisis and that breakdown will make space for extra-constitutional measures,” said Mr Hasan. “This order, and its timing, exposes the Supreme Court as a partisan actor.”

A poisoned chalice? Pakistan’s elected prime ministers

Zulfikar Ali Bhutto

Prime Minister 1973-77

Bhutto’s ascension to power in 1973 marks a short spell of democratic reform for Pakistan after decades with generals at the helm. It comes to an abrupt end in 1977 when protests erupt over alleged vote rigging and General Zia ul-Haq stages a coup. He sends Bhutto to the gallows two years later on trumped-up charges of conspiring to murder a political opponent.

Benazir Bhutto

Prime Minister 1988-90/1993-96

Military rule ends when General Zia dies in a mysterious plane crash in Punjab province. Bhutto’s daughter Benazir leads her father’s Pakistan Peoples Party (PPP) to victory. Her first term is cut short when she is dismissed on corruption charges, but she returns to power for a second term. Attempts to run for a third, however, are cut short in 2007 when she is killed in a suicide bombing in Rawalpindi.

Nawaz Sharif

Prime Minister 1990-93/1997-99

A former minister under General Zia, Sharif wins elections in 1990, but is forced out by the military in 1993. He returns to power in 1997, but is again ousted in a coup, heralding a long spell with General Pervez Musharraf in power. Sharif spends years in exile to avoid charges Musharraf pursues against him, but returns for polls in 2008, with his party performing well.

Yousuf Raza Gilani

Prime Minister 2008-12

Musharraf finally relinquishes power in 2008 and the PPP wins elections. Bhutto’s widower, Asif Ali Zardari, is nominated to President and Raza Gilani becomes Prime Minister. He is forced out by the Supreme Court after refusing to pursue corruption charges against Zardari.