ISLAMABAD (AP) — Pakistan’s anti-corruption chief refused a Supreme Court order to arrest the prime minister in a graft case Thursday, citing a lack of evidence, in the latest clash between the government and the country’s top court.

The arrest order issued Tuesday intensified the sense of political crisis in Pakistan, where a firebrand Muslim cleric has been leading thousands in an anti-government protest in the heart of the capital, Islamabad, for the past four days. The cleric said Thursday would be the protest’s last day but warned ominously that he would let the crowd decide how to respond if officials didn’t meet his demands, prompting the government to send a high-level delegation to meet with him.

The growing instability is likely a concern for the United States, which relies on Pakistan for help in its fight against Islamic militants and efforts to stabilize neighboring Afghanistan.

Fasih Bokhari, chief of the National Accountability Bureau, told the Supreme Court during a hearing that the initial investigation into the corruption case against Prime Minister Raja Pervaiz Ashraf and more than a dozen others was flawed and he needed more time to determine whether the premier should be arrested.

The case involves kickbacks that Ashraf allegedly took during his time as minister of water and power that were related to private power stations built to provide electricity to energy-starved Pakistan. The prime minister has denied the allegations.

The investigating officers ‘‘were not able to bring incriminating evidence but relied on oral statements which are not warranted in the court of law,’’ said Bokhari, who was appointed to his post by President Asif Ali Zardari.

Chief Justice Iftikhar Chaudhry questioned why the anti-corruption chief needed more time since the case against the prime minister has been pending for about a year. He ordered Bokhari to bring the case files back to the judges later in the day so they can determine whether there is incriminating evidence.

‘‘There may be some who consider themselves above the law, but let me make it clear there is no one above the law,’’ Chaudhry said.

Another judge, Sheikh Azmat Saeed, chided Bokhari, saying he was acting more like a defense lawyer than a government prosecutor.

The Supreme Court has clashed repeatedly with the government over the past year, especially over an old corruption case against Pakistan’s president in Swiss court. Pakistan’s Supreme Court convicted Ashraf’s predecessor, Yousuf Raza Gilani, of contempt of court for refusing to reopen the case and ousted him from office.

Critics of the court have accused the chief justice of hounding the government because of bad blood between him and the president. Some have also suggested he is working in concert with Tahir-ul-Qadri, the cleric who has paralyzed key areas of Islamabad in recent days with his anti-government protest. Both men have denied the allegations.

Qadri has galvanized many Pakistanis with his message that the nation’s politicians are corrupt thieves who care more about lining their pockets than dealing with the country’s pressing problems, such as electricity shortages, high unemployment and deadly attacks by Islamic militants.

Despite heavy rain, thousands of Qadri’s supporters remained camped out on the main avenue running through Islamabad for the fourth day Thursday after spending a chilly night wrapped in blankets on the street or sleeping in neat rows of tents.

Qadri is demanding the government be dissolved and replaced with a caretaker administration formed in consultation with the judiciary and the military. He also wants electoral reform to weed out corrupt politicians.

The government has refused his demands, calling them unconstitutional. The cleric’s critics accuse him of working with the country’s powerful army to delay elections expected this spring. Qadri has denied the allegations.

The cleric delivered a new deadline for the government to comply with his demands by Thursday afternoon and warned that if it failed to do so, the crowd would take matters into its own hands.

‘‘We gave a chance to law, we gave a chance to democracy, and now we are giving the last chance to peace,’’ said Qadri, who spoke from inside his bulletproof container, sheltered from the driving rain.