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 body parts, kept in cooler boxes in the man's apartment, included at least two severed heads, the police said.
Body parts thought to belong to eight women and a man had been concealed under cat litter inside coolboxes.
Police found the bodies of eight women and one man in cold-storage containers on Monday and Tuesday, as they were conducting a search on suspicion of the man's involvement in the disappearance of a young woman.
According to local media, Shiraishi moved to the apartment in August and contacted his victims by tweeting that he would help with their suicide plans.
"It's true that I tried to hide the bodies of the people I killed to destroy evidence", Shiraishi was quoted as saying by the police. The woman was last seen walking along with the man last week. The brother later used her Twitter account password and found that she had been exchanging messages with Shiraishi, investigative sources said. But, lately the country has been ripe with tragic, high-profile murders.
Shiraishi threw out some of the body parts as rubbish, along with the victims' belongings, reports said.
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.
When they knocked on the door, he answered, and the police saw boxes inside.
Shiraishi's neighbors expressed shock and disbelief at the news that nine bodies had been discovered in his apartment.
"In August, there was a smell, similar to that from sewage, coming from his residence", says a male company employee who lives in the same apartment building as Shiraishi.
Shiraishi's case is not the first involving the killing of suicidal people identified online. The Asahi Shimbun reported one other case of a killer who had found his victim on a suicide-related website.