Bay of Plenty Rugby Union rugby operations manager Neil Alton said a rule, which had been in place for a long time, meant the final would be played in Tauranga.
He said because there was another final on the same day - the premier development final between Tauranga and Greerton - those finalists were also taken into consideration when choosing the venue.
He said each finalist was given points and the sub-region with the most points got to host both finals. Alton said the three Western Bay teams Mount, Tauranga and Greerton (four points) trumped the sole Central Bay side Whaka (two points).
That meant the finals will be held at a neutral venue in the Western Bay, namely Tauranga Domain, he said.
"It's not a home ground for Mount and it is not a home ground for Whaka. It is a neutral ground for Whaka," he said.
He said it could be seen as benefiting Mount Maunganui but that was simply how the system currently worked.
Whaka coach Ngarimu Simpkins said that system needed to change.
"I definitely think the system needs to be looked at again," he said.
"It only seems right, having finished as the top side, that we have earned the right to host the final. It would have been a great result for us."
He said there were fewer teams in the Central Bay compared with the Western Bay, so the odds were stacked against them ever hosting the final.
Whaka assistant coach Kopae Irihei said it was disappointing for Rotorua rugby supporters.
"I am totally shocked.
"I thought it would be held here or at the [Rotorua International] stadium, so they have really made it hard for us," he said.
"It is just disappointing for our supporters to fork out and hire more vans again. "
He said it would stop a lot of Rotorua fans from going to watch.
Despite the decision, the coaching staff said they would not use it as an excuse and would be up for the challenge on Saturday.
The current rule will be up for discussion between the union and clubs at the end of the season.
