Striker Muto sustained a right knee injury playing for German club Mainz in the Europa League in midweek, while Usami is one of a string of attacking players on the injury list at Bundesliga outfit FC Augsburg.
Japan, bidding for a sixth consecutive World Cup finals appearance, made a disappointing start to the final stage of Asian qualifying with a stunning 2-1 home loss to the United Arab Emirates.
The four-times Asian champions rebounded with a 2-0 victory over Thailand but can ill afford another slip up against Iraq in Saitama on Thursday ahead of their crunch Group B clash with Australia in Melbourne the following Tuesday.
Usami and Muto came on as substitutes against Thailand but Saito will do well to get on the bench with Europe-based forwards Keisuke Honda, Shinji Okazaki, Genki Haraguchi and Takuma Asano already in the squad.
The top two from both of Asia's six-team groups qualify directly for Russia in 2018 with the two third-placed teams playing off to decide who takes on a CONCACAF nation for another spot in the finals.
(Reporting by Nick Mulvenney, editing by Peter Rutherford)
