Mohsin Ali Naqvi, who was a Deputy Director in the Geological Survey of Pakistan, was shot dead at Saryab Road in Quetta, the capital of Balochistan capital, state-run radio reported.
Police officials told the media that they were treating the incident as a case of sectarian killing.
Balochistan has witnessed a wave of sectarian violence against Shias as well as attacks by Baloch nationalist groups.
The gunmen who attacked Naqvi escaped. His family said he had no enmity with anyone.
Last month, a Shia judge was shot dead with his driver and bodyguard in Quetta.
Dozens of members of the Shia Hazara community have also been killed by extremist groups.