The probe concluded that NSA had eavesdropped on political leaders and officials in Germany, France, Sweden and Norway.
According to DR, the alleged set-up between the United States and Denmark was codenamed "Operation Dunhammer". It allegedly allowed the NSA to obtain data by using the telephone numbers of politicians as search parameters.
DR said its report was based on interviews with nine unnamed sources, all of whom were said to have had access to classified information held by the FE. The military agency allegedly helped the NSA from 2012 to 2014.
Merkel's spokesman, Steffen Seibert, said that "the German government has taken note of the reporting. It is in contact with all relevant national and international authorities for clarification."
Seibert said Merkel found out about the latest spying report as a result of questions from journalists.
Reports in 2013 that the NSA listened in on German government phones, including Merkel's, prompted a diplomatic spat between Berlin and Washington that soured otherwise good relations with Barack Obama's administration.
Merkel at the time declared that "spying among friends" was unacceptable. Still, there were also reports that Germany's own BND intelligence agency may have helped the US spy on European companies and officials.
Former NSA contractor Edward Snowden, who revealed details of the secret US eavesdropping programmes in 2013, reacted to the DR report with a sarcastic tweet in Danish: "Oh, why didn't anyone warn us?"
In a written comment to DR, Danish Defence Minister Trine Bramsen said the government cannot discuss intelligence matters.
She added the present government has "the same point of view" as the former Social Democratic government led by Helle Thorning-Schmidt who was in power during that period: "The systematic wiretapping of close allies is unacceptable."
In August, Bramsen relieved the head of the country's foreign intelligence service, among others, after an independent watchdog heavily criticised the spy agency for deliberately withholding information and violating Danish laws.
Denmark has two intelligence agencies, the Danish Defence Intelligence Service, which is also responsible for military intelligence, and the domestic Danish Security and Intelligence Service, known by its Danish acronym PET.