Tokyo Metropolitan Police are investigating the death as a possible case of suicide.
Around 4:40 am local time, a police officer who was not the Prime Minister Fumio Kishida found the 25-year old man at the West Gate Guard Station.
According to police, the deceased officer was on duty as a guard at the residence during the incident.
If you or someone close to you is suffering from suicidal feelings or mental health issues, there is help available.
Contact information for crisis centres around the globe is available from the International Association for Suicide Prevention and Befrienders Worldwide.
After a recent attack against Kishida, the Japanese authorities are on high alert.
A man threw what appeared to be a homemade smoke bomb towards the Prime Minister during a speech last month. Kishida wasn't hurt, but observers were alarmed by the fact that the suspect was able to get so near him and use what looked like a homemade weapon.
This was less than a month after the assassination last July of Shinzo Abe during a speech in Nara, a western city.