This time, Honda has decided to use Hayden, who does not have commitments in Superbikes, where he is fifth in the standings, 234 points behind Jonathan Rea.
Given the time constraints, Honda used test rider Hiroshi Aoyama in Japan, but he struggled with race pace and finished 15th, a minute behind the winner, his teammate Marquez.
Pedrosa is still recovering after undergoing surgery on Saturday in Barcelona following the collarbone fracture he suffered on Friday at Motegi after a huge crash.