The clash comes after four soldiers and four policemen were gunned down by Lashkar-e-Jhangvi (LeJ) militants over the past two days.
Those attacks took place in the city of Quetta, Balochistan, an area plagued by infighting between Sunnis and Shias.
Pakistan's military is engaged in a long-running battle against the group.
Khan Wasey, a spokesman for the Pakistani paramilitary Frontier Corps, said: "Three terrorists belonging to LeJ have been killed in an armed clash with Frontier Corps and intelligence personnel."
Balochistan chief minister Sananullah Zehri condemned the killings by the LeJ saying "strict actions" would be launched against terrorists and their supporters.
The LeJ is a Sunni Muslim extremist group originating from the Punjab province. They are supported by the Taliban and carry out attacks throughout Balochistan and along the Afghan border.
Balochistan is Pakistan's poorest and least developed province, and the military there has been accused of torture, kidnapping, and extrajudicial killing of separatists.
Ethnic Baluch activists say the military has also greatly restricted freedom of movement.
Pakistani forces have killed three suspected members of a banned militant group as part of a crackdown following attacks on security personnel.