Johnson was missing from the Cottagers side which ended a run of five successive defeats with a 1-0 victory over the Barclays Premier League's bottom side Portsmouth last night.
"He will have knee surgery in America, when they will go in and see what it is, and then fix it," he said. "There is a risk that he will be out for the rest of the season, but there is also some optimism." He added: "However, the experience of our medical people think it might be (season ending).
"I am disappointed in that, because I was still believing he was going to come back and it would not be that long. Now I may be looking at the rest of the season with a limited and inexperienced group of front players."
Fulham's lack of firepower was evident as Bobby Zamora and debutant Stefano Okaka created few chances between them.
Roy Hodgson's men had to rely on a fortuitous goal from Jonathan Greening to seal the win.