Islamabad, PAKISTAN - Clashes between police and anti-government protesters have continued outside Pakistan’s parliament, resulting in the deaths of at least three people, and injuries to 494 more, witnesses and hospital officials have told Al Jazeera.

Police continued to fire tear gas and rubber bullets at hundreds of stone-throwing protesters, while thousands more remained behind the front lines outside the country’s parliament building in the capital Islamabad.

The protesters, supporters of opposition politician Imran Khan and anti-government cleric Tahir-ul-Qadri, have been camped out outside the country’s parliament since August 15, calling for Prime Minister Nawaz Sharif’s government to resign.

Late on Saturday night, Khan and Qadri ordered their followers to move towards the prime minister’s official residence, prompting hours of intense clashes with hundreds of riot police. Sharif was not present at the residence, remaining at his personal residence in the city of Lahore, where he normally resides.

The clashes in Islamabad continued sporadically into Sunday, with protesters and police hurling stones and expletives at each other from across the roadblocks that divide them. Police also fired occasional volleys of rubber bullets and tear gas.

Khan called on his supporters late in the day to prepare themselves to face the violence again as night fell.

Scores injured

One of the men who died drowned in a ditch adjacent to the protest site, while the other suffered a fatal penetrative wound, Dr Aisha Isani, a hospital spokesperson, told Al Jazeera.

A third man suffered serious penetrative wounds to his head late on Saturday, Dr Isani said, and succumbed to his wounds on Sunday afternoon.

At least 89 policemen were among those injured in the clashes as protesters, mainly Qadri’s supporters, attacked them with sticks, stones and slingshots.

"They grabbed a hold of me when we charged at them, and then hit me with sticks" said Zeeshan Ali, 24, a police officer who suffered wounds on his head, shoulders and hands. "They beat me for 20 minutes, and then I fell unconscious."

Protesters, meanwhile, said that police had fired rubber bullets directly at the crowd.

"Our objective was to remove the roadblock [leading to the PM’s residence]," said Muhammad Yousuf, 27, a Qadri supporter from the town of Bahawalnagar. "We were moving the container when the police started firing [rubber] bullets and tear gas at us."

Yousuf suffered five rubber bullet wounds, in his hands, back and left leg.

Negotiations break down

The government has maintained its overnight stance that it was the protesters who started the violence.

"This clash can only be stopped by those who started it. We have not started this [violence]," Pervez Rashid, the information minister, told local media on Sunday.

Following the outbreak of violence on Saturday night, protesters used their vehicles and other implements to break down the boundary fence around the parliament building, occupying the compounds large gardens.

Rashid went on to say that the government’s doors were still open for negotiations with both Qadri and Khan.

Our objective was to remove the roadblock [leading to the PM’s residence]. We were moving the container when the police started firing [rubber] bullets and tear gas at us. - Muhammad Yousuf, 27, supporter of cleric Qadri

Previous rounds of negotiation have broken down over the refusal of both Khan’s Pakistan Tehreek-e-Insaf (PTI) and Qadri’s Pakistan Awami Tehreek (PAT) to back down from their demand that Sharif quit office.

In a statement released on Saturday, the PM’s office reiterated that there was "no question" of Sharif resigning.

Khan’s PTI alleges massive vote rigging in the 2013 general elections which saw Sharif’s PML-N sweep to power and wants fresh elections. Qadri has called for the government to be overthrown and for a "national government" of technocrats to be appointed to rewrite the constitution.

On Thursday, Pakistan’s powerful military intervened in the crisis, saying it would play the role of mediator between the apparently intransigent positions of the PML-N and the opposing PTI and PAT.

Army Chief General Raheel Sharif’s intervention, however, appears to have little effect on ending the deadlock. General Sharif, no relation to Nawaz, led a snap meeting of the country’s military leadership on Sunday evening to discuss the current crisis.

PM Sharif himself remained silent on Sunday, but did meet with senior party leaders to discuss the situation.

Differences have also emerged within Khan’s own party, as Javed Hashmi, a senior PTI leader, said on Sunday afternoon that he did not support Khan’s call for protesters to face off against police, warning that the country was "close to martial law".

Meanwhile, limited protests were also held by PTI and PAT supporters in Karachi, Lahore and other cities in Pakistan.

Follow Asad Hashim on Twitter: @AsadHashim