One of his bodyguard's was wounded, police said.
Khalaf, who has already survived six assassination attempts since his appointment in June, was put in control of Basra on December 18 and ordered to battle Shia fighters in the area.
US and British military commanders have praised the police chief for being one of the most able leaders of Iraq's security forces.
The province of Basra, which accounts for more than 80 per cent of Iraq's oil exports, has been the scene of a turf war among rival Shia factions.
Security operations in Basra are seen as a test of whether the Iraqi authorities can keep peace without the assistance of US and British troops.
Violence has subsided since British forces pulled out of the city in September.