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.
Ramis appeared to twist his knee in a tackle with Dimitar Berbatov and Martinez expects bad news for the summer signing.
"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.
"The way he created a relationship with Gary Caldwell, he coped with Berbatov and Mladen Petric.
"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."
It was an unfortunate end to a hard-fought encounter, which Wigan deservedly took a point from.
Giorgos Karagounis' fantastic first-half strike put Fulham ahead but Franco di Santo levelled in equally impressive fashion, cutting in from the left to unleash a fierce drive past Mark Schwarzer.
"I am very, very pleased with the performance," Martinez said.
"I think we started the game really brightly and carried a very good threat in the the attacking third.
"The goal came a little bit against the run of play and from that moment on it would be all too easy to accept the momentum was Fulham's.
"But I thought we restricted Fulham really well and they only had two shots on target - the goal and right at the end, with Maynor Figueroa's special clearance.
"In between those two actions I thought we were the better side. We defended really, really well.
"We restricted Fulham and carried a real good threat. I thought Mark Schwarzer was man of the match and I think his save to deny Shaun Maloney was maybe the save of the season.
"It had to be something special to beat him and I was glad Franco di Santo got the reward."
Martinez might have left Craven Cottage satisfied but Fulham counterpart Martin Jol certainly was not.
Today's result means the Londoners have now failed to win in four successive home matches in all competitions, with the last victory coming against Newcastle on December 10.
"It is always the same story," Jol said. "You go one up and you need another goal but cannot score another goal and then you are vulnerable.
"It is easier said than done but when you are 1-0 up you still have to dominate the game.
"We had a little problem to contain them and they had players in the pockets but we are a big team at the back.
"But we needed a second goal and we did not score a second goal. It was the same against Southampton when we needed second goal and didn't score and they scored an equaliser.
"We have a problem in our balance but we have quality and that will pull us through but we have to score two goals.
"Last year, if we scored one goal it was decisive. This year most of the time, it wasn't decisive."