Mitch Inman (C) of the Rebels addresses players. Photo: JULIAN SMITH/EPA

Melbourne Rebels coach Tony McGahan will leave at the end of the Super Rugby season, the club said Thursday as he pays the price for the team's poor performances.

The team, which is under threat of being axed from next year's competition, have managed only one win so far this season under the weight of a crushing injury toll.

The Melbourne side is currently locked in a stand-off with the Australian Rugby Union, which wants to cut either Western Force or the Rebels as part of Super Rugby's plan to slim down from 18 to 15 teams.

"This has been a particularly tough year on and off the field and we are grateful for the resilience and determination Tony has shown to keep the players and staff focused on performance," said chief executive Baden Stephenson.

"Tony's legacy will remain with the club through the program that he has established, processes that are in place and upcoming talent he has nurtured and we wish him the best in his future direction."

McGahan has been coach for four years but has failed to take them to the finals.

He has, however, unearthed eight Wallabies including last year's Australian Super Rugby player of the year, Sean McMahon.

"I look forward to following the Rebels as a club and help in the transition of the new coach and ensuring the transition is as smooth as possible," he said.

McGahan has two games remaining in the Super Rugby season – against Western Force on July 7 and Argentina's Jaguares a week later.