He told police he killed each "on the day he met" them after tweeting his intention to help them kill themselves, according to several media outlets citing police sources.
Police discovered the nine heads on October 30 while searching for a 23-year-old woman who vanished six days earlier from Hachioji, a suburban city located in the western portion of the Tokyo Metropolis.
Investigators discovered the missing woman had recently posted a tweet that said: "I'm looking for someone to die with me", local reports said.
Authorities then discovered CCTV footage showing the woman taking a train at JR Hachioji Station and then walking with a man strongly resembling Shiraishi at Sobudai-mae Station on the Odakyu Line near his home on October 23.
"I met her for the first time at the time of the incident," Shiraishi was quoted as having told police.
He has reportedly admitted to murdering her and police believe her head is among the nine found at the apartment.
Two heads were found in an Esky near the front door while the others had been placed inside coolers and toolboxes throughout the apartment.
Shiraishi is specifically accused of destroying the body of an unidentified victim and abandoning their remains in a cooler between August 22 and October 30 but expected to face many more charges, including several counts of murder.
"I dismembered the corpses in my bathroom and dumped the flesh and internal organs as trash," the suspect was quoted as having told police.
A saw was also confiscated from inside the apartment on the second floor of a two-storey complex.
The MPD has set up a special taskforce to identify the remains using DNA testing and other methods.
The case has stunned Japan and photographs of the nondescript "house of horrors", located in the quiet southwestern suburb of Zama, have been splashed across the nation's front pages.
"Killing room," read the headline in the Nikkan Sports tabloid while the Sports Nippon went with "One murder a week".
The apartment is located in a residential area about 500 metres from Sobudai-mae Station, and is close to the US military's Camp Zama.
According to The Mainichi Daily, Shiraishi moved in as recently as August 22 and began killing almost immediately, contacting his victims by tweeting that he would help their suicide plans.
Neighbours later said they had noticed a foul smell coming from the flat.
Local residents told media that Shiraishi moved into the apartment two months ago from his parents' home about 2.5 kilometres away, also in Zama.
Prior to his relocation, his father had reportedly contacted a real estate agency, saying: "I want my son to move in right away".
While Japan prides itself on its low crime rate, it is no stranger to high-profile violent crimes.
Last month 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.
WHERE TO GET HELP:
If you are worried about your or someone else's mental health, the best place to get help is your GP or local mental health provider. However, if you or someone else is in danger or endangering others, call 111.
If you need to talk to someone, the following free helplines operate 24/7:
DEPRESSION HELPLINE: 0800 111 757
LIFELINE: 0800 543 354
NEED TO TALK? Call or text 1737
SAMARITANS: 0800 726 666
YOUTHLINE: 0800 376 633 or text 234
