The slain employees were the director and deputy director for DHL in Afghanistan, said Zemeri Bashary, the Interior Ministry spokesman.
Gerold Beck, a DHL spokesman at its headquarters in Bonn, Germany, confirmed the two slain were not German citizens but he declined to release further information.
"We are working together with authorities (in Kabul) to clarify the situation, but can not say anything further at this point," Beck said.
Bashary said police arrested 13 people after the incident, including DHL guards and employees. He said it was not yet clear who was behind the shooting or why it happened.
A Taliban spokesman said the militia was not involved.
The attack follows the slaying in Kabul of a dual South African-British citizen by gunmen earlier in the week. The Taliban immediately claimed responsibility for that shooting, saying the woman had been proselytizing.
Security has deteriorated around Afghanistan in the last two years, although violence against Westerners in the capital has been relatively rare.
Also Saturday, international security companies warned their clients in Kabul about intelligence indicating that militants were planning a large-scale attack on a restaurant frequented by Westerners.