A police bomb squad started examining the Batik Air plane after it landed in South Sulawesi with 122 passengers from the eastern Indonesian city of Ambon, transport ministry spokesman J.A Barata told AFP.
An air traffic controller in Ambon had received a bomb threat via text message as the plane headed toward its intended destination of Jakarta, he said.
"A bomb threat forced a Batik Air flight to make an emergency landing this morning in Sultan Hasanuddin airport in Makassar," he said.
Batik Air is part of Lion Group, which runs Indonesia's biggest low-cost carrier Lion Air.
Barata said the result of the police search was not yet known.