It was initially thought the 29-year-old would be sidelined for three months, but he must now wait until February at the earliest for his return.
"Bobby's had his operation. He will now be in bed with his leg elevated for two weeks," Hughes said. "The operation showed ligament damage so we're probably now looking at five months."
He added: "We want to help Bobby get back quickly and there are no concerns over his ability to get back to the level he was before he got injured."
With Andy Johnson still several weeks away from a first-team return, Fulham must now rely on impressive new signing Moussa Dembele to spearhead their attack.