In 1943, during World War II, he ran the Japanese Naval research program into nuclear technology, known as the F-Go Project.

Early on in the war Commander Kitagawa, head of the Navy Research Institute's Chemical Section, had requested Arakatsu to carry out work on the separation of Uranium-235.

The work went slowly, but shortly before the end of the war he had designed an ultracentrifuge (to spin at 60,000 rpm) which he was hopeful would achieve the required results.

[4][5] After the Americans atom bombed Hiroshima, he was transferred to Navy Minister Mitsumasa Yonai to form an investigative commission.

After the war, his reports and artifacts were largely destroyed or confiscated by the occupying GHQ, which brought much protest from Arakatsu and the international community.