The 22-year-old Queenslander, who is leaving the Belgium-based team for Pramac Ducati at the end of the season, had surgery in Barcelona on Saturday to insert a plate and eight screws.
"Miller already has some mobility in the injured leg, but will head back to Andorra today to start an intense programme of physiotherapy designed to get him back on the bike for the Australian Grand Prix," the non-works team added.
The Australian round at Phillip Island near Melbourne is on Oct. 22, the weekend after Japan.
"Obviously I'm both disappointed and frustrated to have to sit out the Japanese Grand Prix through an injury sustained while training, especially as it wasn't even a crash," said Miller.
Miller, winner in the Netherlands last year but currently 12th in the championship, is the third rider to suffer injuries away from the racetrack in recent weeks.
Italian Valentino Rossi, a nine-times world champion, broke his right leg while training on an off-road bike at the end of August while Britain's Cal Crutchlow needed surgery after severing a tendon while cutting cheese at home.
Yamaha's Rossi returned to racing barely three weeks later, finishing fifth in Spain on Sept. 24.
(Reporting by Alan Baldwin in London, editing by Christian Radnedge)
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