"We have held anti-terrorism drills and have worked closely with the police agency so we are confident of delivering a safe race," said race president Koji Sakurai.
About 30,000 runners are expected to take part in the race through the streets of Tokyo. Police will be among those runners as part of new security measures.
Islamist militants threatened Japanese people everywhere after the slaying of two Japanese hostages last month.
The Tokyo race is one the World Marathon Majors along with Boston, Chicago, London, Berlin and New York.
The Boston Marathon in 2013 was the target of a terrorist attack that killed three people.
The Tokyo race will include 64 "Running Police" officers, aged in their 20s to 40s, who will watch for suspicious movements or behaviour. They will wear white vests bearing the word "POLICE" and will each run about 10 kilometres while carrying special batons, whistles and tear-gas spray.
Runners will also be prohibited from carrying plastic bottles.