"Our anti-aircraft weapons engaged a number of enemy drones that were targeting facilities and sites in the city," the military source said, accusing the Rapid Support Forces of being behind the attack.
Eyewitnesses reported hearing explosions in the north, west and south of the city.
On Thursday, a Sudanese military source said that a drone attack targeted the Flamingo naval base in Port Sudan for the fifth consecutive day.
Port Sudan has enjoyed relative calm since the outbreak of war between the army and the Rapid Support Forces in April 2023, which caused mass displacement, famine, and ethnic killings.
The Red Sea city became a base for the government allied with the military after the Rapid Support Forces overran large areas of the capital, Khartoum, at the start of the war.
The drone strikes on Port Sudan opened a new front in the war after the army had recently made gains in the capital and central Sudan.
Since mid-April 2023, the Sudanese army and the Rapid Support Forces have been waging a war that has left more than 20,000 dead and approximately 15 million displaced and refugees, according to the United Nations and local authorities. Research by American universities estimates the death toll at approximately 130,000.