The four-day test began at Kasumigaseki station on the Tokyo Metro on Monday. The district is home to many government offices.
The scanner is about 60 centimeters in height, and has been installed near a ticket gate. The device detects electromagnetic waves from a person’s body and belongings and reveals images.
The ministry will test whether the scanner is capable of detecting mock explosives and other items hidden beneath clothing of people cooperating with the tests.
Although, the ministry adds that the scanner cannot discern the exact nature of potential explosives.
A senior ministry official says they want to determine if the system can be introduced at rail transport points without interfering with the flow of riders.
The test comes as three passengers were stabbed by a man on a Shinkansen bullet train last June. One died and two were wounded in the attack.