"They (the drones) were met with anti-aircraft missiles," the source said on condition of anonymity because they were not authorised to speak to the media.
An AFP correspondent reported a series of explosions early Wednesday and then a cloud of smoke coming from the direction of the Flamingo base, just north of the city.
War has raged since April 2023 between Sudan's regular army and the paramilitary Rapid Support Forces, which the government has called a "proxy" of the United Arab Emirates.
Port Sudan on the Red Sea coast had been a safe haven city, hosting hundreds of thousands of displaced people and United Nations offices, until Sunday when drone strikes blamed on the RSF began.
Drones struck across Port Sudan on Tuesday, hitting the main port, the city's main power station and the country's last functioning international civilian airport.
Nearly 600 kilometres (373 miles) south, "three drones attempted to strike airport facilities" in the eastern city of Kassala, near the border with Eritrea.
Eyewitnesses told AFP they could hear explosions from anti-aircraft missiles west of the city, which has also come under repeated attacks this week.
Since it began, the war has killed tens of thousands, uprooted 13 million and created the world's largest hunger and displacement crises.
The RSF has not commented on the attacks this week on Port Sudan, about 650 kilometres from its nearest known positions on the outskirts of the capital Khartoum.
Wednesday's attack comes a day after Sudan cut ties with the UAE, accusing it of supplying weapons used by the RSF to strike Port Sudan and declaring the Gulf country an "aggressor" state.
The UAE has long denied supporting the RSF, despite reports from UN experts, US politicians and international organisations.
The attacks on Port Sudan have raised fears of disruptions to humanitarian aid deliveries in Sudan, where famine has already been declared in some areas and nearly 25 million people are suffering dire food insecurity.
Nearly all aid into the country flows through Port Sudan, which the UN on Tuesday called "a lifeline for humanitarian operations", warning of more "human suffering in what is already the world's largest humanitarian crisis".
According to experts, the RSF has increasingly relied on drones since losing territory -- including nearly all of Khartoum in March -- in order to signal its reach and obstruct the army's supply lines.
The war has effectively split Sudan in two, with the army controlling the centre, north and east while the RSF holds nearly all of Darfur and parts of the south.
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