The September 2011 letter from the International Security Assistance Force headquarters in Kabul to regional commands makes specific mention of the phone and email surveillance programme run by the US National Security Agency (NSA), said the Bild daily.
The NSA director had instructed the US military to coordinate surveillance operations in Afghanistan, said the letter from ISAF headquarters to the commands, including the northern Mazar-i-Sharif, led by the German Bundeswehr.
The Bild daily also reported this week that Germany's foreign intelligence service the BND had previously requested PRISM communication data in searches for German kidnap victims abroad.
Many Germans are angry that their emails, phone calls, web searches and other data have been captured and stored under the NSA programme, details of which were leaked by fugitive intelligence contractor Edward Snowden.
Merkel has testily told Washington that "we are not in the Cold War anymore" but also repeatedly defended the role of secret services in keeping citizens safe and preventing terrorist attacks.
Snowden, on the run from the US government, has been marooned at a Moscow airport since June 23 and yesterday filed an application for temporary asylum in Russia. Venezuela, Bolivia and Nicaragua have said they would be open to offering refuge to Snowden.