On Monday, Tokyo Metropolitan Police entered the second-floor residence, located in the Midorigaoka area, and found seven ice coolers inside the premises to contain the body parts belonging to eight women and one man.
Takahiro Shiraishi, 27, has admitted killing all eight of his female victims after meeting them on Twitter earlier this year.
The woman posted a message on the social networking site in late September seeking someone to help her take her own life, to which the suspect allegedly answered with a "Let's die together" message.
In Japan, a low-crime country, it is the grimmest such case since a former employee of a centre for the disabled went on a knife rampage there, killing 19 people past year.
Shiraishi has, for now, been arrested on the charges of dismembering only one body.
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Investigators found what they believe are the bodies of nine people, in cool boxes while searching for a missing 23-year-old woman, a police spokesman said.
The woman's brother reported her disappearance to police the next day. Shiraishi's neighbors noticed "foul smells" near his apartment lately. When her boyfriend came looking for her, Shiraishi told the police, he killed him, as well. She agreed to contact Shiraishi and to invite him to meet her at a train station while the police observed.
Shiraishi remains under arrest on suspicion of attempting to dispose of the bodies, a charge usually brought by the Japanese authorities while they gather sufficient evidence to lodge a murder charge. "During the course of the investigation, the heads of nine bodies have been discovered", the police told a local TV channel.
Shiraishi's case is not the first involving the killing of suicidal people identified online.
Although Japan has one of the lowest crime rates in the world, it has seen some high-profile killings recently.