Pakistani authorities arrested nearly 1,000 supporters of jailed former prime minister Imran Khan who stormed the capital this week to demand his release, the city's police chief said on Wednesday.

Khan's aides alleged, without immediately providing evidence, that hundreds had suffered gunshot wounds during chaotic scenes overnight in the heart of Islamabad as police dispersed protesters led by Khan's wife who had broken through security barricades. They also said thousands had been arrested.

Islamabad's police chief, Ali Rizvi, denied that live ammunition had been used during the operation, which he said police had conducted alongside paramilitary forces.

Rizvi said 600 protesters had been arrested in Tuesday's operation, bringing the total since the protest sit-in began on Sunday to 954.

He said weapons, including automatic rifles and tear gas guns, were seized from the protest site where thousands had gathered. The site was cleared in a matter of hours.

Ali Amin Gandapur, a top Khan aide and chief minister of Khyber Pakhtunkhwa province who was a part of the protests and fled when the operation began, accused the authorities of using excessive force against protesters who he said were peaceful.

He said "hundreds" had sustained bullet wounds.

Pakistan's information minister and an Islamabad police spokesman did not respond to a request for comment on the allegation.

"Both Imran Khan's wife and I were attacked directly," Gandapur told a press conference in the city of Mansehra, in the province he rules.

Khan's wife Bushra Khan escaped unhurt. Khan's party, Pakistan Tehreek-e-Insaf (PTI), had said she would address the press conference with Gandapur, but she did not appear even though the event was delayed by hours.

PTI spokesperson Zulfikar Bukhari PTI said earlier that the protest seeking Khan's release had been called off, citing what he called "the massacre". But Gandapur said the protest would continue until Khan himself called it off.

t least six people - four paramilitary soldiers and two protesters - had been killed in the protests before the overnight clashes, according to PTI.

But the office of Interior Minister Mohsin Naqvi denied this. "As of now, no death has been reported, and the claims circulating regarding any such incidents are baseless and unverified," it said in a statement.

Visiting protest sites on Wednesday, Naqvi said law enforcement agencies had successfully cleared protesters from the site of the sit-in and other areas of the capital.

He called on PTI to provide any evidence of the firing of live ammunition by security forces, and said it had not provided any details of deaths of its supporters.

Geo News and broadcaster ARY both said security forces had raided the site in central Islamabad in complete darkness, and that a barrage of tear gas had been fired.

The protesters were almost completely dispersed, they added.

On Wednesday, city workers were clearing debris and moving away some of the shipping containers authorities had used to block roads around the capital.

The red zone - the fortified area that is home to parliament, the diplomatic enclave and other key buildings - was empty of protesters, but several of their vehicles were left behind, including the remains of a truck used by Bushra Khan that appeared charred by flames.

The PTI had planned on maintaining a sit-in in the red zone until Khan, who has been in jail since August last year, was freed.

Pakistan's benchmark share index (.KSE), opens new tab jumped more than 5%, after falling 3.6% on Tuesday on news of clashes.

Prime Minister Shehbaz Sharif told a televised cabinet meeting that the struggling economy could ill afford a paralysing protest that had cost it 190 billion rupees ($680 million) a day.

($1 = 277.8000 Pakistani rupees)

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