Roshan Khalid, the spokeswoman for the governor of Parwan province, said the bodies were found Monday in the Dasht-e-Khon village in the province.
The pair had been shot and killed, Khalid said blaming the deaths on nomads.
The German foreign ministry would not confirm the deaths, with a spokesman saying his office is "tracking all information."
For its part, the Taliban said it did not know of the abduction or the killing, saying it was not responsible.
The two were reported missing in late August, with the German Foreign Minister Guido Westerwelle saying at the time it was possible "they have become victims of a kidnapping."
Westerwelle had declined to provide more information on the identities of the two Germans.
Khalid on Monday said the Germans worked for a non-governmental organization and had come to Salang Pass in the province to mountain-climb.
The village where their bodies were found is about three hours from Salang Pass.
A team was headed to the village Monday to retrieve the bodies, Khalid said. Source