The blockbuster fight was seemingly close to being confirmed over the weekend but the decision has plunged the contest into doubt. Warren suggests that Wilder may have to "step aside" so the unification clash can take place as planned in August.
The promoter told BBC Radio's Today Show: "It is really simple now, Tyson now either goes immediately to the fight with Deontay Wilder or we try to reach an accommodation with Wilder.
"To use a phrase in boxing 'step aside' to allow the fight between Anthony Joshua and Tyson Fury fight to take place.
"I'm sure he'll (Wilder) want as much as possible but that is going to be about a negotiation if we go down that road. It will cost quite a bit of money. Until we reach an accommodation with Wilder's people, I can't say the fight will definitely happen."
Despite the complications, Warren is confident that "common sense will prevail" and that Fury will be able to fight Joshua.
He said: "We are working hard to get that over the line. We were talking last night. If we can't get it done Tyson will go to the fight with Wilder. They are the only two options. The arbitrator says that Tyson has a contractual commitment and he has to fulfil that. He is tied up legally.
"I expect common sense will prevail so we are going to try and make the fight between AJ and Tyson. That is the fight everyone wants to see. We are going to do our best to get it over the line. That is what everyone has been working towards for a long time now."