Sudanese security forces systematically planned and coordinated a series of deadly attacks that killed up to 241 pro-democracy protesters and injured hundreds more at a Khartoum sit-in last year, an inquiry has found.

Authorities “purposefully pre-positioned” state security forces armed with tear gas, whips and assault rifles in the month before the protests began, and “intentionally targeted” medical personnel and facilities during and after the protests, according to the New York-based advocacy organisation Physicians for Human Rights (PHR), which led an investigation into the violence.

The findings were based on interviews with 30 survivors of the 3 June massacre, eyewitness accounts, and analysis of thousands of still and video images of the protests, among other sources of information. They contradict previous theories that the attacks on the protest camp were spontaneous, or the work of “rogue” military personnel, as a government-led inquiry indicated.

“The June 3 massacre against Sudanese civilians at the hands of government security forces is an egregious violation of human rights,” said Phelim Kine, PHR’s director of research and investigations.

“Security forces’ horrific tactics – sexual violence, including rape, use of tear gas, whips, batons, and live ammunition – killed and critically injured hundreds of civilians. To support the national commission charged with investigating these crimes, the Sudanese legal and human rights community, as well as international bodies such as the United Nations and the African Union, must conduct further investigation into the full scope of government-perpetrated violence on June 3.”

Sudanese forces deployed to disperse the Khartoum sit-in are seen around army headquarters on 3 June, 2019. Photograph: Ashraf Shazly/AFP/Getty Images

Grassroots pro-democracy protests began in December 2018 in the centre of Khartoum in opposition to three decades of autocratic rule by Omar al-Bashir. The unrest continued after the president was ousted by military generals in April 2019 as protesters called for power to be ceded to civilians.

On 3 June, armed men in military uniform – many of whom declared themselves to be members of the Rapid Support Forces – stormed the peaceful sit-in that had been camped for months outside the military headquarters, shooting, stabbing, beating, raping and humiliating protestors.

Interviewees told PHR how security forces taunted them while beating, burning, and cutting them. One witness described an attempt by armed men to sexually assault him after they detained and tortured him, cutting open a healed wound and putting out cigarettes in it. Several interviewees said they had seen women gang-raped in broad daylight. Others described being shot at, beaten with whips and batons, and suffering severe post-traumatic stress disorder and anxiety.

PHR said some survivors would suffer from a lifetime of chronic pain and disability as a result of their injuries.

One interviewee, Muna, recounted how she had been wearing skinny jeans during the protests. She reported that a soldier from the Rapid Support Forces – a paramilitary force heavily armed by Bashir – grabbed her and said: “How do we get her pants off her? Give me a blade so we can tear it off her.”

A doctor interviewed by PHR said he was directly targeted by soldiers, who pointed automatic weapons at him as they yelled: “You’re the reason for all this chaos and this whole mess … You’re the reason why the country’s like this. You’re the reason why we kill people. You’re the reason why people die.”

The attacks were used to “intimidate and silence those demanding civilian rule and major reforms in Sudan”, said PHR’s director of policy, Susannah Sirkin, who contributed to the report.

“As doctors and their organisations were at the forefront of calls for change in Sudan, they were a target. As those who treated injured protesters, or received bodies in the morgues, they were doubly targeted. As credible witnesses to gross human rights violations and their physical and psychological impacts, they were triply targeted.”

The report echoed similar findings, published by Human Rights Watch in November, which concluded that “the number of forces deployed in the operation against the sit-in – estimated in the thousands – suggests official operational planning”.

Medical expert Rohini Haar, who serves as research and investigations adviser at PHR, said: “This pattern of targeted attacks on healthcare is a recurring weapon used by Sudanese security forces that violates the obligation and rights of medical personnel to treat those in need, threatens the lives of medical workers, and has a devastating impact on civilians.”

PHR is calling on UN member states to sanction the Sudanese officials responsible for the human rights abuses and for Sudan’s civilian-military government to include human rights, rule of law and accountability protections in the nation’s new constitution.