"It was a serious malfunction", Merkel told reporters travelling with her aboard the "Konrad Adenauer", a former Lufthansa airlines jet named after post-war Germany's first chancellor.
But a spokesman for the German Air Force said there was no suspicion of any crime, adding: "It's a standard check of the radio equipment that failed".
A senior journalist with the public national television ZDF said Merkel would spend Thursday night in Bonn. Eventually, Merkel and the rest of the German delegation boarded an Iberia flight to complete the trip to Argentina.More news: Russian Federation massing troops, weapons at Ukraine border - Kiev
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German media said that the Chancellor and her Finance Minister, Olaf Scholz, were expected to travel on to Argentina on Friday, possibly on a scheduled flight.
No details were given about the technical problem. Fire trucks with blue lights waited on the runway as the plane landed 30 minutes later before taxiing to the military area of the airport.
Its G36 assault rifle became the butt of jokes after reports it had trouble firing straight at high temperatures, and is being phased out.
There were few early signs of trouble on board the flight, aside from a frozen video screen that would normally show the progress of the flight.