The problem occurred when the aircraft's landing gear failed to retract shortly after it took off for Brussels, the network said.
The prime minister himself confirmed the technical malfunction to another news agency.
The plane circled over Sofia for about an hour before making an emergency landing back at the airport shortly after 8:30 pm (1830 GMT), according to local media.
Borisov was expected to leave later on Wednesday on another plane to attend Thursday's European Council meeting in Brussels.
