Authorities were quizzing 27-year-old Takahiro Shiraishi, who has reportedly confessed to hacking the flesh off the bodies and throwing it out with the trash, then sprinkling cat litter over the remains in an effort to cover up the evidence.
The grisly case has stunned Japan, which enjoys an extremely low crime rate, and pictures of the nondescript house in a quiet residential area were splashed across the country's front pages.
"Killing room," splashed the Nikkan Sports tabloid. "One murder a week," wrote the Sports Nippon.
Shiraishi has told police he contacted his prey via Twitter and killed them "on the day he met" them, according to several media citing police sources.
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He moved to the flat in Zama, a southwestern suburban of Tokyo, on August 22 and contacted victims by tweeting that he would help their suicide plans, the Mainichi Shimbun daily reported.
Police were led to Shiraishi and his secret stash of bodies while investigating the disappearance of a 23-year-old woman.
This woman had earlier tweeted "I'm looking for someone to die with me", local reports said. Authorities then discovered a link between her and Shiraishi.
Neighbours later said they had noticed a foul smell coming from the flat.
The 27-year-old suspected killer has now been turned over to prosecutors, a policeman told AFP.
For now, he has been charged with improper disposal of one body but police are searching for evidence he killed all nine.
While Japan prides itself on its low crime rate, it is no stranger to high-profile violent crimes.
Earlier in October, a 32-year-old father was arrested on suspicion of stabbing his daughter to death. He also admitted torching the house in which his wife and four other children were found dead.
In Japan's bloodiest crime for decades, Satoshi Uematsu faces charges of killing 19 people and attempting to kill or injure 24 others at a disability centre near Tokyo in July 2016.
In 1997 a 14-year-old schoolboy decapitated an 11-year-old acquaintance and placed the head at the gates of his school.
