Der Spiegel reported Saturday that the agency, known by its acronym BND, tapped a satellite phone conversation Kerry made in 2013.
The magazine says the agency also recorded a conversation between Clinton and former U.N. Secretary-General Kofi Annan a year earlier.
Without naming its sources, Der Spiegel says the calls were collected accidentally and the three officials weren’t directly targeted.
The magazine also cites a confidential 2009 BND document listing NATO member Turkey as a target for German intelligence gathering.
Neither the BND nor the U.S. embassy in Berlin immediately responded to requests for comment Saturday.