"Today, Emenike underwent a successful operation on his meniscus and will miss four to six weeks," the Russian Premier League side said on their website.
Emenike, who finished as joint top scorer at February's African Nations Cup, won by Nigeria, will miss his country's World Cup qualifiers against Kenya and Namibia next month.
Nigeria and Malawi top Africa's Group F with five points each from three matches.
Emenike, who turns 26 next week, will also miss the end of the Russian league season, with just four matches remaining.
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