McAteer was close to tears after been carried off on a stretcher late in the first half.
Republic of Ireland manager Mick McCarthy said: "Jason was very down afterwards.
"But I have told him he will be all right and I sincerely hope he will be.
"It may be just bruising. He is going for a scan to check for ligament damage."
The incident follows on the heels of the controversy surrounding captain Roy Keane, who was sent home on Thursday after a row with manager Mick McCarthy.
The Republic came from behind to win the warm-up game in Izumo's Hamayama Stadium 2-1, both goals coming from Robbie Keane.
McCarthy went into the game saying he wanted a good workout and for no injuries.
But as well as McAteer's worrying knee injury, his Sunderland team-mate Kevin Kilbane hobbled off.
"Kevin just got a little twist on his ankle and Ian Harte has a sore foot but both will be okay - no danger," said McCarthy.
The Irish manager made little attempt to hide his anger about the crude challenge on McAteer.
And the revelation that the offender Tulio was from Cameroon - Ireland's first opponents in the World Cup - did little to lighten his mood.
When told that Tulio was going to the Irish changing room to apologise, McCarthy said: "I do not think he would be welcome there right now.
"It was a bad tackle, I have no doubt about that. And in the spirit of a friendly match there was no need for it."