Tensions between Puntland and Galmudug soared last month after Galmudug said a US strike aimed at Shabaab jihadists had in fact killed 13 of its soldiers.
Galmudug authorities accused neighbouring Puntland of feeding the US false information that led to the air strike.
Fighters from the two regions exchanged machine gun fire and fired anti-aircraft weapons today in the town of Galkayo, which is divided between the two administrations and historically rival clans.
Puntland authorities in a statement accused Galmudug forces of attacking them "to retaliate" for the US strike.
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Mohamed Hassan Sahal, a spokesman for the Galmudug administration, told AFP the fighting broke out in an argument over land.
"Puntland administration deployed forces at a disputed construction site last night and the fighting erupted this morning. It stopped now but six people from the two sides were killed during the clashes", he said.
The US Africa Command (AFRICOM) confirmed carrying out a "self-defense" strike near the town of Galkayo on September 28, when Al-Qaeda linked Shabaab fighters attacked a Somali force and their US advisors.
Witnesses said the fighting today continued for several hours.
"The fighting stopped but it can resume anytime because no one is mediating between the two sides so far, people will start fleeing for their lives if it resumes," resident Abdikarim Ali told AFP.