Japanese police have found nine mutilated bodies hidden in containers with their heads cut off and flesh stripped in a suburban Tokyo flat, media reported Tuesday.

Tokyo police have arrested 27-year-old Takahiro Shiraishi who 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.

According to local media, Shiraishi told police he had chopped up the bodies in a bathroom, while a saw was found in his room.

The suspect reportedly told investigators he had "dumped cut flesh and organs in the trash," prompting fears he was a serial killer as police believe he killed all nine victims, according to NHK.

Journalists gather in front of an apartment (partially covered with a blue sheet) where the headless bodies were found. Photo: AFP

Police and journalists swarmed around the nondescript apartment in the quiet residential neighbourhood of Zama, as locals struggled to comprehend how an act of such violence could have occurred so near them.

"It's really cruel. He used a saw to dismember the bodies or something. He must be abnormal to have done such things," said neighbour Hideaki Hosogaya, 83.

The Sankei Shimbun newspaper quoted another neighbour as saying he had smelled an odour he had "never smelled before".

"I thought it was the smell of sewage," he said.

Police used blue tarps to block views inside the two-storey building, and covered windows of the second-floor room where the bodies were discovered.

Japanese social media users were quick to draw parallels with Halloween. One Twitter user wrote: "Nine dismembered bodies found on the day of Halloween. Humans are definitely scarier than ghosts."

Another said: "What a psychotic event on Halloween. I don't think I could bear 10 minutes with nine dead bodies around."

'Die with me'

Authorities had been investigating the disappearance of a 23-year-old woman and discovered a connection between her and Shiraishi.

This woman had earlier tweeted "I'm looking for someone to die with me", according to the Sankei Shimbun daily.

Other media said Shiraishi and the woman had connected via a website featuring information about suicides.

A CCTV image showed Shiraishi and the 23-year-old woman walking together last Monday, NHK reported.

She had been missing since September 21 and her older brother reported her disappearance to police, according to the Asahi Shimbun.

Police gather in front of the apartment. Photo: AFP

When police visited the apartment, they originally found two heads inside a cool box at the entrance before making the grisly discovery of the other body parts, according to Jiji Press.

"During the course of the investigation, the heads of nine bodies have been discovered" inside various coolers and containers in the apartment, private TV network TBS said.

For the time being, police arrested Shiraishi on a charge that he dismembered one body and placed it inside a cooler, a charge that he was not contesting, according to a spokesman at Tokyo Metropolitan Police.

"He has said 'I dismembered a body and placed it inside a cooler and poured cat litter over it. It was meant to hide the body that I killed and to hide evidence'," the spokesman told AFP, declining to elaborate.

Japan prides itself on a low crime rate but 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.