Corendon Airlines said it wanted to "emphasise that no emergency situation occurred and that at no point were the passengers, flight crew or aircraft in any danger".
The incident forced a brief suspension of operations at Nuremberg Airport, where the plane was headed, the airport said.
Authorities said fighter jets were scrambled to escort the passenger plane.
Flight operations later returned to normal.
"From the cockpit, the code '7500' (hijacking case) was transmitted, and furthermore, the pilot could no longer be reached by radio. For safety reasons, various alarm scrambles were then triggered," police earlier said on X.
An airport spokesperson said six flights were delayed and two inbound flights were diverted to other airports as a precaution.
The alert comes less than a month after the co-pilot of a jet bound for Israel from Dubai attacked the pilot with an emergency crash axe, with the United Arab Emirates' prosecutor general calling the incident a "terrorist attack".
The airline said the emergency code had been transmitted on Tuesday while the plane, a Boeing 737-800, was in Croatian airspace "due to a brief malfunction in the radio communication system".
"The situation was immediately monitored, investigations were promptly initiated and all necessary preparations were made. The aircraft landed safely at Nuremberg Airport," it said.
The airport said earlier on its website: "Flight operations are currently suspended due to an in-flight emergency. Flight XR 456 from Corfu to Nuremberg has since landed safely."
An airport spokesperson had no additional information.
A possible drone sighting had already disrupted air traffic at the airport overnight into Tuesday, the airport said in a separate statement.
German authorities have also been on heightened alert since a failed attack involving an explosives-laden drone at a German airport in August, which authorities blamed on Russia.
Russia denied any involvement.
with AP
