BERLIN — Eleven years ago, as the Iraq war raged, the National Security Agency quietly turned over to its German counterpart a sprawling electronic spying station in Bavaria. The transfer came with a deal: In consultation with the Americans, German spies would continue operating the station to intercept communications in Europe and the Middle East and share what they picked up.

For the third time in less than two years, Washington and Berlin are at loggerheads over that arrangement. After a month of intelligence leaks, awkward telephone calls between top aides to President Obama and Chancellor Angela Merkel of Germany, and demands that the government here release data about what spying Germany did at America’s bidding, Ms. Merkel is once again seeing the practical and political difficulties of disentangling intelligence relationships between the two countries.

Ms. Merkel’s critics accuse her of being the N.S.A.’s lap dog, and her intelligence services of perhaps facilitating spying on at least two European companies, the European Aeronautic Defense and Space Company and Eurocopter, both part of what is now the Airbus Group.

Adding to the political pressure, emails between American and German officials have been leaked, all but confirming that a much-publicized effort in 2013 and 2014 to create rules that would halt any American snooping on German soil was largely a sham. The Germans who pushed for the agreement optimistically called them “no-spy” rules; the Americans considered them impossible from the start.