The Japan international was carried off on a stretcher after being hurt in a challenge from Kevin Mirallas in Latics' stunning 3-0 FA Cup quarter-final win at Everton last weekend.
It is yet another setback for the 20-year-old, who has made just seven appearances for the club since joining on loan from Arsenal due to injuries.
Manager Roberto Martinez told the club's website: "It was a terrible challenge. We are waiting on the scan but we are not very positive on it.
"We think it will need a long recovery period and maybe he will even need surgery.
"We need to be a little bit expecting the bad news.
"He is very fortunate he has not got a broken leg because of the nature of the challenge.
"We feel he ruptured the ligaments. We will have to wait and see but he doesn't seem to have an opportunity to finish the season."
Martinez delivered a more positive update on Callum McManaman, who was one of the stars of Wigan's first-half display at Goodison Park but limped off soon after scoring the second goal.
Martinez said: "Callum McManaman is recovering well and probably it is more a matter of a week - five days to 10 days - that he is going to be out.
"We will see how he recovers day by day. The ankle is swollen but it is more of a normal injury."
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