Yusuke Katayama, a chubby, bespectacled former IT worker, was accused of sending online messages in 2012 that threatened mass murders at elementary schools and warning of bombs in an airplane and at a shrine.
On Thursday he changed his plea in the case to guilty, according to Japanese press reports. He had been out on bail but was taken back into custody this week.
"It's all true," NHK TV quoted Katayama as telling the Tokyo District Court, a reversal of his not-guilty plea in February.
The online messages were sent via a virus copied to the computers of other people, leading police to make four false arrests.
But what really captured the attention of the Japanese public in the so-called "remote-controlled virus case" was that a message criticizing police -- as well as the source code for the virus -- had been placed in the collar of a stray cat on tiny Enoshima Island, southwest of Tokyo.
Police used surveillance footage of Katayama hanging around the cat as evidence in his arrest in 2013.
After he was released on bail in March, Katayama appeared at a press conference at The Foreign Correspondents' Club of Japan in Tokyo, complaining that he had been "treated 100 percent as a criminal by the media."
But the case took a dramatic turn when email was sent to media outlets last Friday claiming to be from the real culprit in the case. The email was sent while Katayama was in court for a hearing.
Investigators allege that they had followed Katayama and found a smartphone buried along a riverbank in Tokyo that was used to send the email. They also claim Katayama's DNA was on the phone.
Prosecutors took him back into custody on Tuesday after the court revoked his bail.
"In order for the defendant to feel the gravity of what has been done, it's extremely important that the victims in this series of incidents appear in court," defense lawyer Hiroshi Sato told a press conference, adding that Katayama apologized for his actions.
Katayama has apparently made suicidal remarks, and his lawyers may seek a psychiatric evaluation.