General Atta Muhammad, leader of the mainly Tajik Jamiat faction, said 50 of his men were wounded or killed in fighting with rivals from the mainly Uzbek Junbish group on Wednesday.
The Junbish is led by feared regional commander Abd al-Rashid Dostum.
The fighting erupted in and around the town of Fayazabad, near Mazar-e-Sharif and Dostam's stronghold of Sheberghan 120km to the west.
Junbish official Sayyid Nur Allah, a deputy of Dostam, said the fighting started after Jamiat militiamen attacked a Junbish commander travelling towards Mazar-e-Sharif.
Nur Allah said three Junbish were killed and four injured in the initial attack.
Tensions between the rival militias have been growing since the weekend when two Junbish commanders were allegedly kidnapped by Jamiat forces in Kodibark, 20km west of Mazar-e-Sharif.
Junbish had sent reinforcements to Fayzabad, Muhammad and Nur Allah said.
News of the fighting prompted shopkeepers in Mazar-e-Sharif to down shutters, as residents feared the clashes would spread to the city.
Muhammad sent tanks late on Wednesday through Mazar-e-Sharif to head west towards the fighting at Fayzabad, city police commander General Isa Iftikhary said.
Some tanks would remain in Mazar-e-Sharif to defend the city against any possible Junbish attacks, Iftikhary added.
The city has previously suffered sporadic clashes between the militias.
Foreign troops are due to be
deployed beyond Kabul
Vying for control
Former communist general Dostam and his rival Muhammad have been vying for control of northern Afghanistan along with a third ethnic Hazara militia, Hezb-i Wahdat.
Dozens of people have been killed this year in clashes between the various factions.
Two militiamen were killed and one injured in a separate Jamiat-Junbish clash, early on Wednesday in Almar district of Faryab province, 260km southwest of Mazar-e-Sharif.
Clashes between the two militias, which support President Hamid Karzai, are a continual headache for the central government which is trying to assert its authority beyond Kabul.
Disarming 100,000 militiamen, rebuilding the army and reining in regional commanders are priorities for Karzai in his efforts to improve security and extend the reach of his government to the provinces.
A Japanese-funded programme to disarm and demobilise the militiamen is due to start later this month, following reforms at the ministry of defence which was dominated by ethnic Tajik anti-Taliban commanders.
The reforms, including 22 new high-level appointments, are intended to make the ministry more representative of Afghanistan's ethnic and regional diversity.