The FIM commissioned an independent report to investigate the "general situation" in Japan following the earthquake, tsunami and nuclear emergency which stuck the country in March.
They revealed last month that they expected the race to be given the green light after receiving an encouraging preliminary report on the potential dangers of staging the race.
And after receiving the final report, the FIM confirmed in a statement on Tuesday: "The FIM and [MotoGP commercial rights holder] Dorna Sports have now received the official detailed and final report.
"Based on this report, the FIM and Dorna Sports confirm today [Tuesday] that, subject to there being no further serious incidents, the Grand Prix of Japan will take place on October 2 as planned."
The report - which looked at radiation levels from a number of sources including air, environment and food - claims that "the radiation risk during the race event is negligible".
The Motegi circuit is situated less than 100 miles from the site of the Fukushima nuclear plant, which suffered meltdowns and nuclear leaks in the wake of the devastating magnitude 9.0 quake and subsequent tsunami on March 11.
Reigning MotoGP world champion Jorge Lorenzo and current series leader Casey Stoner have already stated that they do not intend to take part in the race, which has been rescheduled from its original date of April 24.