Government forces have conducted a major operation freeing most of the hostages, but estimate more than 30 are still being held.
The Taliban have so far not commented on the incident in Aliabad district in the volatile province of Kunduz, where the insurgents briefly overran the provincial capital in a stunning military victory last year.
"The Taliban shot dead 16 passengers and they are still holding more than 30 others," said Sayed Mahmood Danish, spokesman for the governor of Kunduz.