Johnson damaged his anterior cruciate ligament in training on Tuesday, and this new blow comes just months after he fought his way back to fitness after a season ruined by a niggling pelvic injury.
"We are really disappointed for Michael, he has had a terrible run of injuries and this has come from a very innocuous situation in training. His foot caught in the turf, the knee hyperextended and he has done significant damage.
"His season is over, he had worked really hard to get back to a level where I was considering him for games again, certainly at this busy Christmas period and he was very much in our thoughts.
"He is not going to be available for quite some time and it is going to be difficult for him. He showed real strength of character to come through the year out that he had last year, he will have the operation on the 21st and he'll have landmarks to get through with his rehab after then."
Speaking to the press at the Carrington training ground on Friday lunchtime, the Manager also confirmed that Wayne Bridge will be out of action after the extent of his knee injury was discovered this week. The left back was stretchered off during last Saturday's win over Chelsea after damaging medial ligaments, and is set to be out until the New Year.
His season is over, he had worked really hard to get back to a level where I was considering him for games again, certainly at this busy Christmas period and he was very much in our thoughts.
...the boss on Johnno...
"Bridgey has opened up his knee and the liklihood is that he will miss the Christmas period," said Hughes. "His injury is one that can show signs of improvement quite quickly but it's always the last 5-10% of the injury that needs to resolve itself."
Bridge's absence could see Sylvinho handed his first league start, but Hughes has other options with both Gareth Barry and Joleon Lescott having decent experience at left-back.
He continued, "I've got a number of options but I would have no qualms whatsoever about putting Sylvinho in there, but Gareth has knowledge of that position as well. It's disappointing to be missing Bridgey but we have enough quality to replace him."
There is better news regarding Craig Bellamy and Vladimir Weiss after the pair were struck down with swine flu and forced out of City's last game.
"Craig and Vladi are OK, they have had a few days of feeling a little bit rough but they have come through after training in the last couple of days," he concluded.