The surveillance was allegedly conducted by a listening post of the Special Collection Service, run jointly by the National Security Agency (NSA) and the Central Intelligence Agency, said the Sueddeutsche Zeitung.
The eavesdropping programme "works worldwide in American embassies and consulates, mostly in secret," it said, citing documents provided by fugitive former NSA intelligence contractor Edward Snowden.
The alleged spying on Merkel, made public Wednesday by the German government, sent shock waves though the country and was roundly condemned by legislators and in the media.
Germany's Foreign Minister Guido Westerwelle on the same day called in the US ambassador and then demanded Washington provide straight answers on the allegations.
German news weekly Der Spiegel this year reported that Special Collection Service surveillance devices could be hidden in US embassies around the world, again citing Snowden documents.
In August, a German police helicopter conducted a fly-over of the US consulate in Frankfurt to search for suspected listening posts, it said.
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