Takahiro Shiraishi, 27, has admitted killing all eight of his female victims after meeting them on Twitter earlier this year.
The paper writes he was already serving a suspended sentence for sex-related crimes when the grim discovery was made.
The police are expected to file murder charges later.
His first victim was another woman whom he got in touch with via Twitter, offering to assist her suicide wish, then killing her boyfriend to silence him, according to the media reports, including NHK public television.
According to news reports, the police discovered body parts from eight women and one man in Shiraishi's apartment, along with a saw, ropes and an awl, apparently used to restrain and cut the bodies. "I dismembered a body and placed it inside a cooler and poured cat litter over it".
Police believe one of the bodies is believed to belong to a 23-year-old woman from Hachioji City. "I'm looking for someone to die with me", she posted on the website.
They are working to identify the victims.
Egypt: 55 policemen killed in gunbattle with militants
The Muslim Brotherhood, once Egypt's largest opposition movement, has long denied involvement in the attacks on the authorities. BBC reported that more than 50 police officers were killed during clashes, while local media said 35 citing security sources.
A man who lived on the same floor as Shiraishi told the Japan Times he had noticed an "odd smell" when he walked past the apartment.
Kyodo news agency said the missing girl is believed to have come into contact with Shiraishi via Twitter, after she posted the message: "I want to die but doing so alone is awful".
Shiraishi's case, involving social media suicide pacts, connections to Tokyo's notorious red-light district and neighbours who did not report a noxious smell coming from the suspect's apartment for months, has the hallmarks of a grotesque thriller novel or horror movie.
"I thought it smelled like sewage", he said.
Shiraishi told the police that he later invited the woman to come alone to his apartment, where he killed her.
Shiraishi told police that he dismembered the bodies in his bathroom, and disposed some of the body parts out with the rubbish, Kyodo News agency reported.
