Nishimiya death comes at a time when Japan-China relations are worsening because of contending claims of sovereignty over a group of uninhabited East China Sea islands, currently under Japanese control.
The cause of his death had not been determined, but Nishimiya had collapsed in his home near Tokyo last Thursday just two days after he had been named the new envoy to China. He had hospitalized since then. Police had ruled out any play, Kyodo said.
Nishimiya had served as a minister at the Japanese Embassy in Beijing and had been scheduled to take over as ambassador from Uichiro Niwa.
Tensions between the two countries have heated up after Japan last week nationalized the Senkaku Islands, which are called Diaoyu Islands by China.
Kyodo reported Nishimiya, as deputy foreign minister in charge of economic affairs, had been in charge of Japan's preparations for the Asia-Pacific Economic Cooperation forum summit in Vladivostok, Russia.
China's official media also carried reports on Nishimiya's death.