The bodies of dozens of slain protesters have been pulled from the Nile in Khartoum and taken to an unknown location, opposition activists have claimed, saying 101 people were killed across Sudan during a deadly crackdown on pro-democracy rallies.

Feared paramilitary group the Rapid Support Forces (RSF) allegedly retrieved at least 40 corpses from the river on Tuesday, according to Sudan Doctors’ Committee, who organised the main sit-in in the capital that was cleared the day before.

Protesters separately told The Independent they witnessed the paramilitaries hurling corpses into the river in the capital after opening fire on civilians.

Eyewitnesses also claimed to have had seen the paramilitary group and other forces shoot at hospitals in Khartoum, flog demonstrators with whips, and set alight protest tents – with fears that anyone hiding inside may have been burnt alive.

One medic, who asked not to be identified for security reasons, said their teams had documented soldiers raping seven female doctors and protesters during the flare-up in violence.

Military HQ occupied by anti-government protesters in Sudan Show all 20 1 /20 Military HQ occupied by anti-government protesters in Sudan Military HQ occupied by anti-government protesters in Sudan Protesters rally outside the military headquarters in Khartoum to demand that President Omar al-Bashir step down Reuters Military HQ occupied by anti-government protesters in Sudan Alaa Salah leads the protest against President Omar al-Bashir Lana Haroun/Twitter Military HQ occupied by anti-government protesters in Sudan Protesters run from tear gas deployed by security forces as they take part in a demonstration to demand the departure of the Sudanese government EPA Military HQ occupied by anti-government protesters in Sudan Sudanese protesters rally outside the military headquarters in Khartoum on April 8 Sudan Congress Party Military HQ occupied by anti-government protesters in Sudan Sudanese protesters rally outside the military headquarters in Khartoum on April 10 Reuters Military HQ occupied by anti-government protesters in Sudan Alaa Salah, a Sudanese woman propelled to internet fame earlier this week after clips went viral of her leading powerful protest chants against President Omar al-Bashir, addresses protesters outside of the military headquarters in Khartoum AFP/Getty Military HQ occupied by anti-government protesters in Sudan Sudanese protesters march on the military headquarters in Khartoum on April 8 AFP/Getty Military HQ occupied by anti-government protesters in Sudan Demonstrators attend a protest rally demanding Sudanese President Omar Al-Bashir to step down outside Defence Ministry in Khartoum, Sudan April 10, 2019. REUTERS/Stringer NO RESALES. NO ARCHIVES Reuters Military HQ occupied by anti-government protesters in Sudan Sudanese protesters pray as they rally outside the military headquarters in Khartoum AFP/Getty Military HQ occupied by anti-government protesters in Sudan Sudanese protesters chant slogans as they march in protest against President Omar al-Bashir Reuters Military HQ occupied by anti-government protesters in Sudan Sudanese protesters rally outside the military headquarters in Khartoum on April 8 AFP/Getty Military HQ occupied by anti-government protesters in Sudan Sudanese protesters rally outside the military headquarters in Khartoum on April 8 AFP/Getty Military HQ occupied by anti-government protesters in Sudan Sudanese protesters climb onto a military vehicle beside soldiers during protests in Khartoum AFP/Getty Military HQ occupied by anti-government protesters in Sudan Security forces deploy tear gas to disperse protesters against the Sudanese government Reuters Military HQ occupied by anti-government protesters in Sudan Sudanese protesters rally outside the military headquarters in Khartoum on April 8 AFP/Getty Military HQ occupied by anti-government protesters in Sudan A wounded protester rests during a demonstration in front of the military headquarters in Khartoum AFP/Getty Military HQ occupied by anti-government protesters in Sudan A Sudanese protester shows bullet cartridges as protesters gather in Khartoum AFP/Getty Military HQ occupied by anti-government protesters in Sudan Protesters march on the military headquarters in Khartoum Sudan Congress Party Military HQ occupied by anti-government protesters in Sudan Sudanese protesters march on the defence ministry in Khartoum to demand that President Omar al-Bashir step down Reuters Military HQ occupied by anti-government protesters in Sudan A Sudanese protester picks up waste during a demonstration in front of the military headquarters in Khartoum AFP/Getty

The Independent could not independently verify the reports.

In total, the Sudan Doctors’ Committee said at least 101 people had been killed and hundreds more injured across the country since Monday, although that casualty toll is expected to rise.

The Sudan health ministry refuted that, saying on Thursday the death toll was "no more than 46".

The deputy head of the military council, General Mohamed Hamdan Dagalo, commonly known as Hemedti, said it had launched "an urgent and transparent investigation" into the recent violence.

"Any person who crossed boundaries has to be punished," he added.

Amid the surge in violence, Sudanese protest leaders dismissed calls from the military for a fresh round of talks, saying the army was “not serious” about negotiations while troops continued to shoot and kill protesters.

“Their vehicles patrol the streets, firing at people,” Mohammed Yousef al-Mustafa, a spokesman for the Sudanese Professionals Association said.

“We will continue in our protests, resistance, strike and total civil disobedience,” he added.

The protesters said this week was the bloodiest eruption of violence since pro-democracy demonstrations succeeded in forcing the military to remove Sudan’s longtime strongman, Omar al-Bashir, from power in April.

Since then, the movement has maintained a sit-in and demanded that the generals hand over authority to civilians.

For weeks, the military and protest leaders negotiated the make-up of a transitional council meant to run the country for three years before elections.

Appearing to lose patience, however, Sudan’s ruling military council cancelled all agreements earlier this week and announced it would unilaterally form an interim government and hold elections within just nine months.

Forces, that did not include the army, then violently stormed the sit-ins on Monday.

Hussam Hilali, a 33-year-old protester who was at the main sit-in by the military headquarters in Khartoum, described the dawn raid as a “massacre” and said the capital was now a “ghost town gripped by fear”, after the RSF set up flying checkpoints across the city.

The infamous paramilitary forces have their origins in the Janjaweed militia that have been accused by human rights groups of carrying out rapes, torture and killings of civilians during the 16-year conflict in Sudan’s Darfur region.

“It was a massacre, we couldn’t count the dead people and the emergency rooms were overflowing,” said Mr Hilali, sharing mobile phone footage of protesters with bloody head injuries being shuttled in blankets from the front line.

“I saw people sprayed by bullets, there were soldiers flogging people with whips,” he added.

He fled to Khartoum’s main Teacher’s Hospital where he claimed the RSF repeatedly tried to storm the building and attack the injured.

“When I went on the roof I saw the smoke, the fire, as they burnt all the tents,” he added.

It was a massacre, we couldn’t count the dead people Hussam Hilali, a protester

His cousin, Khalid, who was trying to approach the sit-in from the north, saw members of the security forces disposing of corpses from a bridge into the Nile.

“He saw at least three bodies thrown into the waters,” Hilali added.

Rabah Silwah, 37 another activist, who also fled to the Teacher’s Hospital, told The Independent two people were shot in the leg and stomach next to her when security forces stormed the sit-in.

She said she feared people were burned to death in tents which were set on fire.

“We are missing a five-year-old homeless kid who used to sit with us in the sit-in. There are reports he was burnt alive. He was last seen running for cover in the tents which were burnt down,” she added.

She said the security forces stormed the hospital several times and opened fire.

“They opened fire on anything and anything, cars, walls everything,” she added.

Also on Wednesday, rebel group Sudan People’s Liberation Movement-North, whose armed wing has been fighting Sudanese forces in the Blue Nile and South Kordofan since 2011, reported that one of its leaders had been arrested.

Yasir Arman, the SPLM-N’s deputy chief, was detained after being taken from the house where he was staying in Khartoum since 26 May.

Four die in Sudan protests as military rulers say they won't allow 'chaos'

Irfan Siddiq, the British ambassador in Khartoum, condemned Mr Arman’s detention as “outrageous” and called for his release.

The United States, Norway and Britain issued a joint statement condemning the Sudanese security forces for the violent attacks, while Saudi Arabia, which has backed the ruling military council, said it was watching developments in Sudan with concern.

A push for the UN Security Council to condemn the killing of civilians and call on the military and protesters to work together was blocked by China and Russia, during a closed-door meeting on Tuesday.

General Abdel-Fattah Burhan, head of the ruling military council, appeared to backtrack on Wednesday, saying the generals were ready to resume negotiations with demonstrators. He added that those responsible for the violent break-up of the sit-in would be held accountable.

However protesters told The Independent they had little faith in the promises of the generals or that any of their demands would be met, adding that they have vowed to keep up a programme of civil disobedience until the army steps down.

“What happened on Monday was a systematic and planned attempt to impose repression on the Sudanese people,” Madani Abbas Madani, a leading activist, said.