Zamora is facing a long spell on the sidelines after fears he had sustained ankle ligament damage in last Saturday's 2-1 victory over Wolves proved correct.
With the England striker and Fulham's most dangerous player out for half the season, the pressure has grown on Johnson to make his comeback.
The club's record £10.5million signing from Everton missed most of last season with a knee injury but is three to four weeks away from a return to first-team action.
Hughes, however, will only pick the former England marksman if he is fully fit.
"We don't want to rush Andy. He's had experience of trying to get back too soon as a consequence of his enthusiasm to be playing," he said.
"Unfortunately in the past he's come back too soon and that's cost him, preventing him from sustaining his fitness.
"We're not of the view that we must bring him back quickly even though we've lost Bobby.
"It's more important for Andy that he's clear in his mind that he's 100% when he does return.
"When Andy does come back he'll be in and around the first team for a significant amount of time and that will help us get through the loss of Bobby."
Johnson has been plagued by knee, shoulder and groin injuries since arriving at Craven Cottage two years ago, but Hughes insists the early indications are there will be no permanent repercussions from his time in the treatment room.
"Andy's been out for a long time but the medical staff have done a really good job on him and he's really positive," he said.
"All the tests we've done show that he's either on a par or even surpassing some of the levels he was hitting before the injury.
"You can measure straight line runs and sprints off the mark, but we haven't tested him in a match situation yet."
Hughes is equally sanguine over Zamora's chances of making a complete recovery from the injury sustained a month after winning his first England cap.
"Bobby's had his operation. He'll be in bed with leg elevated for about two weeks, then he begins the long return to fitness," said Hughes.
"The operation showed there was ligament damage, which we hoped there wouldn't be. We're probably looking at five months plus.
"There's no concern over his ability to get back and play to the same level that he was at before the injury.
"The expertise that surrounds him during his rehabilitation is as good as I've seen at any club.
"It was a big loss losing Bobby. He was the main focus of our attacking play.
"To lose him for the length of time we are means other players will have to step up to the mark."