The test flight was aimed at checking out the air travel control instruments fixed at the airport, aviation officials said.
Being built with Chinese assistance worth USD 210 million, the airport project is to be completed by next year.
Hambantota in the deep rural south of the island nation.
Rajapaksa wants Hambantota, one of the poorest districts in the island, to be the new economic hub.
Massive infrastructure development has been undertaken in the area which includes the construction of a new sea port and an international cricket stadium.