Takahiro Shiraishi, 27, has confessed to killing the victims and cutting them up, a police spokesman said.
Japan has one of the lowest crime rates in the world.
According to police, the woman posted a message on Twitter saying that she was seeking partners with whom to commit suicide as a group.
The police arrested Shiraishi, whose occupation is unknown, on an initial charge of discarding a body.
Photographers surround a police van transporting murder suspect Takahiro Shiraishi.
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Police found the bodies, some covered with cat litter, while searching for the 23-year-old woman who had disappeared after exchanging Twitter messages, allegedly with Shiraishi.
They are now working to identify the victims, fearing that she might be among them. She had been missing since September 21.
Another told the newspaper he had seen Shiraishi several times late at night.
The arrested man admitted that the theft of money was one of the reasons behind the murders - on one occasion 500,000 yen ($A5,746) - and that he duped some of the women in an attempt to sexually abuse them. The brother said she had been thinking of killing herself since the death of their mother in June, and that she had disappeared on October 23 from the group home in Hachioji, a suburb of Tokyo, where she was living.
The police have not yet said whether the woman's remains were among those at Shiraishi's apartment. Authorities then discovered a link between her and Shiraishi.
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Severed heads were found in coolers, according to the AP.
Neighbours told officers that they had noticed a sewage-like smell for at least two months, but that they had not reported it.
"I killed them and did some work on the bodies in order to hide the evidence", the suspect told police, according to Fox News.
Shiraishi's case is not the first involving the killing of suicidal people identified online. A saw was found in one of the rooms of the flat.
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