A police official said a toolbox and saw found in Shiraishi's apartment may have been used to dismember the bodies.
Police arrested 27-year-old Takahiro Shiraishi the same day on suspicion of body disposal.
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.
They said the missing woman contacted Shiraishi via Twitter in late September, seeking a partner for a suicide pact and saying she was afraid to die alone.
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 a year ago.
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Photographers surround a police van transporting murder suspect Takahiro Shiraishi.
He said investigators found the bodies while searching for a 23-year-old woman who had disappeared.
They are now working to identify the victims, fearing that she might be among them. The brother later learned of the suicide site after logging in using her name and password, and found she had been in touch with the suspect. When her boyfriend came looking for her, Shiraishi told the police, he killed him, as well.
An investigation was launched after the woman?s older brother reported her missing to the Takao Police Station in western Tokyo on October 24. 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.
Shiraishi's neighbors expressed shock and disbelief at the news that nine bodies had been discovered in his apartment.
Severed heads were found in coolers, according to the AP. "I thought it was the smell of sewage", he said.