Japanese media said the body was discovered on Sunday after the suitcase had been kept in temporary storage for more than a month to see if the owner would turn up.
The bright yellow suitcase measured 28 by 20 by 10 inches. It was found in an unlocked locker at Tokyo's main train station on April 26. The body is 140 centimeters tall (4-feet, 7-inches) tall.
Police are trying to establish the woman's identity.