The Japanese MotoGP was cancelled over the coronavirus on Monday as organisers said they would concentrate on holding as many races as possible in Europe this year.
The scrapping of the 16-18 October race in Motegi follows the axing of the Australian MotoGP, which was due to be held a week later.
"The situations in Japan and Europe are unpredictable," said Kaoru Tanaka, president of Mobilityland, which owns the Twin Ring Motegi circuit.
"As a result of our discussions with Dorna, the managerial body of the series, we agreed that we have no choice but to cancel the Japanese GP in order to complete the season."
The first 11 races of the MotoGP season have been either postponed or cancelled, and there have been discussions about how to preserve as much as possible of the European calendar.
At the moment, the sport hopes to resume with back-to-back races at Jerez, Spain.
The first, on 19 July, would be the new season-opener, with Dorna suggesting slotting in the second race at the same circuit on 26 July.
A round of the Superbike Championship was also proposed for Jerez on 2 August.
The opening legs, if approved, are most likely to be held without spectators, and with restrictions on the number of people allowed in the paddock.
There have also been talks about holding the French MotoGP, which was scheduled for May, in October instead.
"The MotoGP family is working very hard to be able to restart the racing season and hold as many events as possible, and in the safest way possible," said Carmelo Ezpeleta, CEO of Dorna Sports.
"(MotoGP organisers) have decided that, until mid-November, MotoGP will remain in Europe to do as many European MotoGP events as we are able to.
"Therefore, overseas events, if at all possible, should be scheduled after mid-November - which would be too late in the year for the Motul Grand Prix of Japan to be held."