There was no immediate word on injuries or damage from the Wednesday incident, which occurred during Shinzo Abe's visit to Indonesia, where he was attending the Asia-African summit.
The incident came shortly after a Japanese court rejected a lawsuit to halt the restart of Kyushu Electric Power's Sendai nuclear station, downplaying local residents' concerns over the safety of the plant in the wake of the 2011 Fukushima disaster.
Meanwhile, the Japanese public television station NHK aired footage showing scores of police and officials standing near the quadcopter, which was covered under cardboard and later by a blue tarp.
The NHK reported that the drone was about 50 centimeters (20 inches)in diameter and that it carried a small camera, a water bottle and something that looked like a flare.
Police said that it was not immediately clear who was responsible, adding that they are looking into the possibility that the drone could have crashed during a flight.