Both Tokyo and Beijing are courting the Southeast Asian nations that ring the contested South China Sea, most of which China claims, to gain influence in the strategic region.
The current defence minister and former special forces commander will be sworn in by President Joko Widodo in October.
His election has raised concerns among human rights groups who point to abuses he is alleged to have committed during his time in the military. Prabowo, who was found by a military council to have kidnapped student activists in 1998, denies the accusations.
Prabowo also met Japan’s Minister of Defence Minoru Kihara in Tokyo.
