Johnson dislocated his shoulder in the Europa League clash with Amkar Perm in August and was initially expected to be sidelined for eight weeks.
He returned to first-team duty after three weeks, but Johnson concedes it is likely to be several months before he is free from pain.
"It's a permanent injury," said Johnson. "I've done as much damage as you can do by snapping all six ligaments.
"I just need to get used to the pain as it's still giving me a bit of stick. You can feel it in games.
"It's not a problem if I'm chasing the ball, but if I go shoulder to shoulder with someone and I land on it then it's very sore, for up to 15 minutes.
"Joseph Yobo came into the back of me when we played Everton a couple of weeks ago and it was painful for five or six days afterwards.
"You might see me holding it in games, but that's how it is now. I think within the next three or four months it will settle down and by next season it will be pain-free.
"It's just a case of getting through that period."