West Salem will move to the Mississippi Valley Conference for football only, effective for the 2014-2015 school year.
The WIAA Board of Control held a special meeting on Wednesday, during which West Salem's appeal was denied.
"My reaction is we're very, very disappointed. From our perspective, this was all about our kids and taking care of our kids. It didn't go our way," said West Salem Activities Director LeRoy Krall.
The proposal, which was initially passed in September, also requires mandatory football only crossover games in weeks three and four between the Coulee Conference and the Southwest Wisconsin Conference.
"[The WIAA Board of Control] saw this as the best avenue in serving all of the member schools in that part of the state," said WIAA Executive Director Dave Anderson.
The WIAA Board of Control approved the measure by a vote of 8-0-1. Failure by any school in the three conferences to honor the plan will result in its removal from the football playoffs for four years.
During the hearing, Krall mentioned West Salem would have to decide between moving to the MVC or taking a four year WIAA football postseason ban if their appeal was denied. Their only other option is to become an independent program.
"That would be a very, very drastic step," Krall said following the meeting. "I can't say definitively how we're going to go about this."
West Salem principal Mark Carlson pointed out the Panthers' 8-12 record versus MVC schools since 1999, and that their 2007 state title team, which he called their best-ever, lost to Onalaska.
Representatives from the MVC, including school activities directors and commissioner Terry Erickson reiterated their support for the plan.
"The decision was in the best interest of 20 schools and that was sort of the big picture," said Erickson. "In the long run, this will be a benefit for West Salem, and I really thing that we will be a stronger conference.
"I'm hoping that with time, some of the hostility and the doubt and the emotions die because it opens the door for some great rivalries between West Salem and the MVC."
In addition, the WIAA Board of Control unanimously approved Augusta moving to the Dairyland Conference for all sports beginning in the 2014-2015 school year.