Over 60 officers were deployed in the race in response to concerns over threats of terrorism.
They wore white vests bearing the word “Police”. Each member ran about 10km while carrying anti-terrorism gear in small backpacks.
“If police are there among the runners they may be able to see things more quickly, and runners will be able to take part in the race with a feeling of security,” a police spokesman said.
Tokyo has been on edge following the killing of two Japanese hostages by the Islamic State group last month. Islamist militants threatened Japanese people everywhere after the killings.
Over 36,000 runners took part in the race as organisers were eager to show Tokyo remains a safe place to hold major sporting events.
Signs on marathon bibs identified the police runners, whose caps were fitted with small cameras transmitting images of the scene to police headquarters for real-time monitoring and analysis. The new security measures are seen as a precursor for the 2020 Summer Olympics in Tokyo.
John Coates, vice president of the International Olympic Committee, told a news conference last Thursday that he remained confident of Japan’s ability to provide security for the games.
Each police runner at the Tokyo Marathon covered part of the 42.2-km (26-mile) race and were chosen from a pool of officers with extensive marathon experience.
“All police officers train as a matter of course, since you never know when you might have to run as part of your daily work,” the spokesman has said.
“But these will be people who run quite a lot.”
The Boston Marathon in 2013 was the target of a terrorist attack that killed three people.