Saturday’s fighting comes after months of escalating tensions between the generals and military unrest after an October 2021 military coup.
In a statement, the Sudan Doctors’ Committee said two civilians died at the country’s main airport and another man was shot dead in the state of North Kordofan.
The statement did not specify how the two people died at the airport, which has been a flashpoint in the violence, with the two forces battling to control it.
The group said dozens more were hurt around the country, with some in unstable conditions.
The clashes began on Saturday morning, with both sides blaming the other for initiating the violence.
In the capital of Khartoum, the sound of heavy fighting could be heard in a number of areas, including the city centre and Bahri neighbourhood.
In a series of statements, the Rapid Support Forces (RSF) militia accused the army of attacking its forces at one of its bases in south Khartoum and claimed to have seized the city’s airport and be in control of Khartoum’s Republican Palace, the seat of the country’s presidency.
The group also said it has seized an airport and airbase in the northern city of Marawi, some 215 miles north-west of Khartoum.
Those claims have not been verified.
The Sudanese army said the fighting broke out after RSF troops tried to attack its forces in the southern part of the capital and accused the group of trying to take control of strategic locations in Khartoum, including the palace.
The military declared the RSF a “rebel force” and branded the paramilitary’s statements “lies”.
One official, who spoke anonymously, said fighter jets took off from a military base north of Omdurman and attacked the RSF’s positions in and around Khartoum.
The clashes come after escalating tensions between the military and the RSF in recent months, forcing a delay in the signing of an internationally backed deal with political parties to revive the country’s democratic transition.
Saudi Arabia’s national airline said one of its Airbus A330s was involved in “an accident” after video showed it on fire on the tarmac at Khartoum International Airport amid the fighting.
Saudia said in a statement on Saturday that all its flights were suspended after the incident. It did not elaborate on the cause of the “accident”, though it appeared the aircraft got caught in the crossfire of the RSF and Sudanese soldiers fighting around the airfield.
Another plane also appeared to have caught fire in the attack. Flight-tracking website FlightRadar24 identified it as a SkyUp Airlines 737. SkyUp is a Kyiv, Ukraine-based airline. It did not immediately respond to a request for comment.
Other commercial aircraft trying to land at the airport began turning around to head back to their originating airport.
Tensions between the army and RSF stem from a disagreement over how the latter should be integrated into the military and which authority should oversee the process.
The merger is a key condition of Sudan’s unsigned transition agreement.
However, the army-RSF rivalry dates back to the rule of autocratic president Omar al-Bashir, who was ousted in 2019.
Under the former president, the RSF, led by powerful General Mohammed Hamdan Dagalo, grew out of former militias, known as the Janjaweed, which carried out a brutal crackdown in Sudan’s Darfur region during the decades of conflict there.
In a rare televised speech on Thursday, a top army general warned of potential clashes with the RSF, accusing it of deploying forces in Khartoum and other areas of Sudan without the army’s consent.
The RSF had earlier defended the presence of its forces.
The paramilitary recently deployed troops near the northern Sudanese town of Merowe.
Videos circulating on social media on Thursday showed what appeared to be RSF-armed vehicles being transported into Khartoum, further to the south.
According to a statement from the Sudan Doctors Committee, which is part of the country’s pro-democracy movement, the clashes have led to “varying injuries”.
The military said the fighting has resulted in a number of casualties but gave no further details.
The US ambassador to Sudan, John Godfrey, said he was “sheltering in place with the embassy team, as Sudanese throughout Khartoum and elsewhere are doing”.
“Escalation of tensions within the military component to direct fighting is extremely dangerous,” he wrote.
“I urgently call on senior military leaders to stop the fighting.”
In Saturday’s statement, the RSF said it was contacted by three former rebel leaders who hold government positions in an apparent bid to de-escalate the conflict.
In a joint statement, civilian signatories to December’s framework agreement also called for an immediate de-escalation.
“We call on the leadership of the Sudanese armed forces and the Rapid Support Forces to stop hostilities immediately,” it said.
Sudan has been marred in turmoil since October 2021, when a coup overthrew a western-back government, dashing Sudanese aspirations for democratic rule after three decades of autocracy and repression under Islamist ruler Mr Al-Bashir.
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