A passenger plane preparing to take off from Sudan for Saudi Arabia came under fire on Saturday as deadly fighting rocked Khartoum, the kingdom's flag carrier said.

The Airbus A330 bound for Saudi Arabia "was exposed to gunfire damage... with guests and crew on board" ahead of its scheduled departure to Riyadh, Saudia said in a statement.

"It has been confirmed that all members of the aircraft's cabin crew have safely arrived at the Saudi Embassy in Sudan," the statement said.

"Meanwhile aircraft flying over Sudan have returned and all other flights to and from Sudan have been suspended in order to preserve the safety of the guests and crew."

Clashes broke out on Saturday between Sudan's army and paramilitaries, and the doctors' union reported three civilian deaths, including at Khartoum's airport in the city centre.

The Saudia statement did not mention any casualties in the incident involving its aircraft.

The paramilitaries said they were in control of the airport as well as the presidential place, claims denied by the army.

The eruption of violence came after weeks of deepening tensions between military leader Abdel Fattah al-Burhan and his number two, paramilitary commander Mohamed Hamdan Daglo, over the planned integration of the paramilitary Rapid Support Forces (RSF) into the regular army.

That was a key element of talks to finalise a deal that would return the country to civilian rule and end the crisis sparked by their 2021 coup, which triggered a deepening economic crisis in what was already one of the world's poorest countries.

The Saudi embassy in Sudan "urges all Saudi citizens to remain at home", the state-affiliated Al-Ekhbariya channel reported.

Both the Saudi foreign ministry and the six-member Gulf Cooperation Council, headquartered in Riyadh, issued statements of concern about Saturday's violence.