The fighting erupted between the groups led by Sheher Yar and Khan Said alias Sajna in Shawal, a mountainous area near Afghan border, Tuesday and continued Wednesday, Dawn online reported.
The militants killed on Wednesday were from the Sheher Yar group, the report said.
Rockets and mortars were used in the fighting.
They said that different militant groups were trying to broker ceasefire between the two factions but they have not succeeded yet.
The two groups have reportedly lost about 60 members in battles over the past month.
The Sheher Yar and Sajna groups were involved in a dispute over leadership of militants in South Waziristan, the report said.