The 26-year-old was taken off in the 1-1 draw with Colchester United on Saturday and underwent scans this week.
Now, Clarke has said they expect to miss the striker for the next few months as he also revealed young midfielder Joe Willis has broken a metatarsal in his foot in a reserve game.
"The squad is going to have to be utilised as we've picked up a couple of injuries," Clarke said.
"Josh is going to be out until at least December. Josh is a big name player for us. It's a medial knee injury so he's in a brace at the minute.
"You never know, sometimes these things can heal a bit quicker but we're probably looking at potentially December.
"We also have Joe Willis who has broken his foot in the reserve game. It's a broken metatarsal.
"We'll see how that settles down but like any bone it has to heal. We're hoping it doesn't need surgery and it heals itself. Fingers crossed on that one.
"Joe is one of our good young pros, he's part of the small squad we have. Any player we miss through injury is a big loss.
"The squad's not the biggest – it's quite good on quality, in my opinion. It's a better squad than last year.
"I have to manage players with the Saturday-Tuesday. We want as little injuries as we possibly can but you can't do anything about contact injuries and those two were contact injuries.
"We have to be mindful about the amount of games we have. I'm not a manager to change it for change's sake, I look at everything.
"The squad members are going to be used in force over the coming weeks and months ahead."
With Gordon out of action, Clarke has now set his sights on a 'free loan' signing before today's 5pm transfer deadline.
He is targetting a young striker that has previous loan experience, with as many as five names on his shortlist.
"I'm getting my begging bowl out to be honest with you," Clarke added.
"We know the tough restraints we're under financially with staff on pay cuts and players deferring. Everybody is doing their bit for the football club and the supporters are doing their fantastic bit.
"We know how much funds are tight but I am trying to get a free loan in if possible.
"I'm working to try and get a centre forward with the news about Josh as it leaves us with only two fit centre forwards.
"The youth team players below that are not quite ready for the step up in my opinion.
"We'll be trying to get a centre forward in before the end of play but obviously things are tough.
"I could go and get a free loan but it would be their first time out on loan, very young and very inexperienced. It probably wouldn't help the group.
"I have loads of contacts in the game, I can speak to any club, any manager, any under-23 manager at any club at any level. I've built that myself.
"The fact of the matter is getting that right player and sometimes you have to be a little bit patient and get your begging bowl out and see if there's a good deal to be had for a more established younger lad who has had one or two loans.
"I have a list of four or five today. I'm hoping one of those comes to fruition but no doubt many managers are having the same conversation.
"With a bit of luck we'll have one in by 5pm today."