The commissioner, who is to meet Japanese Science and Technology Minister Nariaki Nakayama Monday or Tuesday, told AFP that he would discuss new European research programs and joint EU-Japanese research project.
But "ITER will be part of the debate", he said, adding that "it is important to discuss at the political level".
Talks are deadlocked among the six parties involved in the International Thermonuclear Experimental Reactor (ITER), a multibillion-dollar test project for clean, inexhaustible energy, over whether to build facilities in Japan or France.
The United States and South Korea support Japan's offer to build ITER in Rokkasho-mura, a northern Japanese village near the Pacific Ocean, while the EU, China and Russia back the bid of the southern French town of Cadarache.
Potocnik's trip to Japan comes a week ahead of a crucial meeting between European research ministers on April 18 in Luxembourg.