The Afghan policeman, who was armed and in civilian clothes, was outside the base in Musa Qala, Helmand province and turned towards the patrol holding his weapon, the NATO-led International Security Assistance Force said in a statement.
"The ISAF patrol opened fire, mistaking him for an insurgent. No insurgents were involved," it said.
"ISAF troops gave first aid, and evacuated the policeman to the nearest medical facility, where he died of his wounds."
An investigation involving ISAF and the Afghan national police was underway.
The statement did not give the nationality of the soldiers involved in the incident.
Britain has 3,300 troops in the south, two-thirds in Helmand where they have faced regular attacks by insurgents.