Marquez, third in the standings with four races left, injured his left hand mountain biking in his native Spain on Tuesday and was operated on in Barcelona earlier on Wednesday, Honda said on their website.
"If post-operation recovery goes as expected, Marc should be fine to ride in the Japanese Grand Prix," they added.
Marquez needed surgery in April after sustaining a similar injury in a training accident while riding a dirt bike.
The 22-year-old, who has won the past two championships, has 184 points from 14 races, with Italian Valentino Rossi leading on 263 ahead of Yamaha team mate Jorge Lorenzo of Spain on 249.
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There are 25 points available for each race win with 20 points for second spot and 16 for a third-place finish.
(Reporting by Iain Rogers, editing by Ken Ferris)
