Police said the suspect, Yusuke Katayama, denies any wrongdoing, Kyodo News reported.
Four other people had been arrested between July and September and suspected of making the threats until investigators realized someone else had been using their computers without their knowledge, the Japanese news service said.
More than 10 email and Internet threats have been made using remotely controlled personal computers, including one threatening mass murder at a comic book event and another against a kindergarten, authorities say.
Katayama is charged with forcible obstruction of business, Kyodo said.
Police, who said Katayama has a 2006 conviction for a similar crime, searched his home Sunday for evidence he sent an email to reporters Jan. 5 that hinted he was responsible for the threats.