"They fired at the vehicle of the army and mistakenly killed six army soldiers," said Mohammad Omar, governor of Kunduz province in north Afghanistan, adding that the incident happened late on Friday night near Chardara district.
A spokesman for the NATO-led force in Kabul said: "There was an incident but we can't confirm any numbers right now." Earlier on Friday three German soldiers were killed in Kunduz and five others were seriously injured in fighting, the German Army Command in Potsdam said.
In February a NATO airstrike aimed at insurgents attacking a joint NATO-Afghan patrol in Kunduz accidentally killed several Afghan policemen.
Germany is the third-largest NATO contributor to the war with some 4,300 troops in Afghanistan, most of them based in northern Kunduz where Taleban attacks and strength have increased over the past year.