They are Deutsche Welthungerhilfe, an association combatting hunger, and the Afghanistan NGO Security Office (ANSO), which keeps aid organisations up-to-date on the situation in the country and makes them security aware, the weekly says in its edition on sale Monday.
Between October 2005 and April this year the BND monitored at least 2,000 e-mails, fax messages and telephone conversations from the two organisations, according to Der Spiegel.
The magazine noted that during this period Welthungerhilfe was headed by Ingeborg Schaeuble, the wife of the German interior minister. In April Der Spiegel reported that the BND had intercepted e-mails between one of its journalists and Afghan Economy Minister Mohammad Amin Farhang in 2006.
The incident sparked Farhang's ire, and sharp criticism by a German parliamentary commission against the BND and its chief Ernst Urlau for undermining faith in the agency. German Foreign Minister Frank-Walter Steinmeier expressed regret to his Afghan counterpart Rangeen Dadfar Spanta.