"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 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 armed forces and the paramilitary Rapid Support Forces, which the army-backed government has called a "proxy" of the United Arab Emirates.
Port Sudan on the Red Sea coast had been a safe haven, 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 power station and the country's last functioning international airport.
Nearly 600 kilometres (375 miles) further south, "three drones attempted to strike airport facilities" in the army-held eastern city of Kassala, near the border with Eritrea, a security source said.
Witnesses told AFP they heard explosions from anti-aircraft missiles west of the city, which has also come under repeated attack this week.
Nationwide, the war has killed tens of thousands of people and uprooted 13 million.
It has also effectively split Sudan in two, with the army controlling the centre, north and east while the RSF holds nearly all of Darfur in the west and parts of the south.
- Aid 'lifeline' -
The RSF has not directly commented on this week's attacks on Port Sudan, about 650 kilometres (400 miles) from its nearest known positions on the outskirts of the capital Khartoum.
The strikes have raised fears of disruption to humanitarian aid across Sudan, where famine has already been declared in some areas and nearly 25 million people are suffering dire food insecurity.
UN relief chief Tom Fletcher said he was "very concerned by ongoing drone strikes on Port Sudan, a hub for our humanitarian operations and key entry point for aid".
Nearly all aid into Sudan flows through the port city, which the United Nations has called "a lifeline for humanitarian operations".
It has warned of more "human suffering in what is already the world's largest humanitarian crisis".
The United States on Tuesday condemned the drone strikes "on critical infrastructure and other civilian targets in Port Sudan and throughout the country".
"These attacks represent a dangerous escalation in the Sudan conflict," the State Department said.
Spain too condemned the attacks, calling them a "violation of international law and a threat to peace efforts".
- 'Advanced weaponry' -
The long-distance drone campaign comes after the RSF lost control of nearly all of greater Khartoum in March, after holding it virtually since the start of the war.
The foreign ministry of the army-backed government described the attack on Port Sudan as "a full-fledged crime of aggression", which it said was carried out with "strategic drones and advanced weaponry".
Sudan has accused the UAE of supplying the RSF with the weapons it has used to strike Port Sudan.
The UAE has repeatedly denied arming the RSF, despite reports from UN experts, US politicians and international organisations.
Sudan's northern neighbour Egypt has historically been the army's strongest backer and, according to experts, still wields significant influence with army chief Abdel Fattah al-Burhan.
During the war, Burhan has drawn closer to Turkey and Iran.
Russia, which previously supported the RSF through its mercenary group Wagner, has pivoted towards the army's camp, with its sights on a Red Sea naval base near Port Sudan.
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