Provincial police spokesman Syed Sarwar Hussaini confirmed that the employees were kidnapped late on Wednesday evening.
Hussaini further added police forces have launched an operation to release the kidnapped employees.
The Taliban militants group has not commented regarding the report so far.
Kunduz is among the volatile provinces in northern Afghanistan where Taliban militants and insurgents from the other militant groups are actively operating in a number of its districts.
Sher Khan Port is located next to Panj River near the border with Tajikistan. The port is considered as the main transit route linking Afghanistan with the Central Asian countries.