The clash is symptomatic of troubles that may lie ahead when a new interim administration, agreed to at UN-sponsored talks in Germany and composed of the politically disparate Northern Alliance and former exile groups, takes power next week.
General Deen Mohammad Joorat of the militarily dominant Northern Alliance said mainstream alliance forces had taken control of Pul-i-Khumri, 260 km north of Kabul, from fighters from the clan of Sayed Jaffar Nadiri.
"There is no more danger of fighting from Nadiri's side any more. We have full control over Pul-i-Khumri and some areas of Kayan after our ground operation with the co-ordination of American planes last night," Joorat told Reuters.
He did not give any details of the fighting.
Pul-i-Khumri is a key industrial city perched on the main highway linking the capital with the north and beyond to Central Asia.
It was controlled for many years by Nadiri, the leader of Afghanistan's minority Ismaeli sect and a member of the Northern Alliance that was driven from power by the Taliban in 1996.
The alliance retook the town from the disintegrating Taliban in the middle of November and Nadiri returned from exile to resume control.
Joorat said fighting began several days ago when opposition to Nadiri's rule came to a head.
American planes originally came to Nadiri's aid and bombed areas controlled by commanders with links with General Fahim, the military chief of the Northern Alliance that swept the Taliban from power.
"That was a mistake," Joorat said. "He (Nadiri) had passed them wrong information, that is why they bombed our places, but afterwards we sorted out the misunderstanding and went after him and drove him out."
Joorat did not rule out the possibility that ethnic Uzbek warlord General Abdul Rashid Dostum had supported Nadiri in his fight against the Northern Alliance.
"Maybe Dostum had a role in it too."
Dostum, who has close links with the Nadiris, is part of the Northern Alliance and controls several key northern provinces, including Mazar-i-Sharif on the border with Uzbekistan.
He and commanders of the Hazara ethnic group have protested against the dominance of supporters of designated defence minister Mohammed Fahim in the new interim government, which takes power on December 22 and is due to rule for six months.
He has warned that no government will have access to northern gas and oil resources if the issue of distribution of key government posts is not sorted out.
He also said he would cooperate with the new administration and its leader, Hamid Karzai, an anti-Taliban member of the southern Pashtun ethnic group from which Afghanistan's ousted rulers drew their support.
