It was the deadliest episode of a months-long protest movement that kicked off in late 2018 and led to the resignation of veteran President Omar al-Bashir in April 2019 and to civilian rule later that year, Al-Jazeera reported.
Thousands of Sudanese protesters had camped outside the army headquarters in capital Khartoum, demanding al-Bashir's removal and kept up their sit-in even after his departure to protest against the military rule.
On June 3, armed men in military fatigues moved in on the protest camp and dispersed thousands of demonstrators. In the ensuing days-long crackdown, many were killed and wounded.
Doctors linked to the protest movement have said at least 128 people were killed in the violence. Authorities gave a lower death toll of 87, and denied ordering the violent dispersal.
But in a scathing report titled Chaos and Fire, the US-based NGO Physicians for Human Rights said the crackdown was a "massacre" that could have claimed up to 241 lives, according to estimates.
"Sudanese security forces launched a series of planned, violent attacks against pro-democracy protesters that killed up to 241 people and injured hundreds more," the report released on Thursday said.
The group said its findings were based on multiple witness testimonies, consultations with health workers, and analyses of thousands of online video footage and images of the dispersal.
"Sudanese security forces were responsible for perpetrating unconscionable acts of violence against pro-democracy demonstrators," said the report.
Those acts included "extrajudicial killings and torture, excessive use of force, sexual and gender-based violence, and the forced disappearance of detained protesters", it added.
Phelim Kine, the group's research and investigation director, called the dispersal "an egregious violation of human rights".
The group called on the United Nations member states to sanction Sudanese officials responsible for the violence.
Al-Jazeera's Hiba Morgan was in the capital when the shooting began last June.
"We were in Khartoum when the attack on the citizens happened, and we do remember hearing the gunshots opened on protesters at the sit-in," she said.
"People ran for their lives and into buildings and hospitals and those were targeted. The report does match up to what we experienced on June 3 ," Morgan added.
In August, Sudan's military and protest-movement leaders formed a civilian-majority body to rule the country for a transitional period of three years.
The new authorities set up an independent commission to investigate the events of June 3, 2019. The team has yet to release its findings.