The conflict has raged since April 15 between army chief Abdel Fattah al-Burhan and his former deputy Mohamed Hamdan Daglo, who commands the paramilitary Rapid Support Forces (RSF).
A witness in Port Sudan said there had been "an exchange of gunfire between the army and a militia led by Sheba Darar", a leader from the local Beja tribe, in the centre of the Red Sea city.
One witness who spoke on condition of anonymity said "soldiers deployed in the area after removing checkpoints set up by the militia", while others reported a "return to calm" soon after.
Port Sudan is home to the country's only functioning airport and hosts government officials as well as the United Nations after they relocated from the war-torn capital Khartoum.
It had been spared from the violence until Monday night's clashes broke out.
For the past three weeks, it has served as the new base for Burhan, who had until late August been holed up in army headquarters in Khartoum, besieged by RSF fighters.
Burhan has since made six trips abroad from Port Sudan in what analysts say is a diplomatic push to burnish his credentials in the event of negotiations to end the conflict.
Darar -- who supported the army at the start of the war before raging against government officials moving to eastern Sudan -- has not announced an alliance with the RSF.
Other tribes in Sudan's east have vowed to support the army.
Across Sudan, the violence has killed at least 7,500 people since April 15, according to a conservative estimate from the Armed Conflict Location & Event Data Project.
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