The 19-year-old full-back, who joined Killie from Villa on a season-long loan last summer, picked up the injury late in the Viaplay Cup semi-final against Celtic and has missed subsequent games against Rangers and Dumbarton.
Ahead of the bottom-of-the-table cinch Premiership game at Ross County on Saturday, McInnes said: "Ben Chrisene from Villa is out.
"He has a serious injury unfortunately, he has torn his medial ligament and is back at Villa this week and he will be back here next week.
"But he will be out for a significant period, unfortunately. He was doing so well for us."
