The Rams manager made no secret of his desire to re-sign the striker on loan after his first spell with the Championship side was cut short through injury.
"It is looking less and less likely the closer we get to the end of transfer window," Clough told the Derby Telegraph. "There doesn't seem to be any movement at Everton in terms of them bringing players in, so it could well be we miss out on him."
Vaughan played two games for Derby during his short stay there in September but returned to Finch Farm due to a knee injury. He has subsequently recovered and been a part of Everton's current resurgent spell of form.
Speaking at the time Clough was hopeful the forward would return once his recovery was complete and has been in touch with David Moyes on a regular basis.
"We talked to Everton on Friday and every week we give them a call to see if anything has changed, which it hasn't at the moment," he said.
"We are planning without James, as much as we would like him to come back."