The Spanish centre-back had to be taken off on a stretcher toward the end of Saturday's 1-1 draw with Fulham at Craven Cottage.
"That is the real negative of the afternoon," the Wigan boss said. "I thought Ivan was outstanding throughout the game.
"I think you are starting to see a centre-half that has adapted to the British game and is someone very, very important.
"I wouldn't want to say anything before seeing the scans, but I fear the worst. He has damaged the ligaments in the right knee and the signs are not great.
"I expect the worst, cruciate ligament. We are going to take him to hospital on the way back.
"Those injuries go from six to seven months, but obviously it is impossible for me to tell yet because we need to get the scans.
"The manner he has done it, the way he has felt the knee opening and the pain he has got in the top of the patella tendon, I do fear the worst.
"We will miss him because he has been a top, top centre-half for us. We've missed him when he had a little niggle and I think he was outstanding today.
"He is a leader and was the captain at his former club. We will miss him and let's hope we've all got the wrong idea and we get good news from the scan."