The motion passing has so inflamed Ruapehu Rugby and Sports Club that president Bruce Cranston sent a letter to the Wanganui Rugby Football Union stating they don't want to contest the trophy they won from 2009-11.
"This has created a non-level playing field and that disadvantages all club teams other than Marist," the letter said.
"Until such time as there is a level playing field, we wish to withdraw from that competition."
Ruapehu will still play their games, but do not want to be in the Weekes Cup race.
Cranston called the vote "despicable" and "disgusting".
"The intent is to make this a one-horse race," he said.
"Should we just make a presentation at the start of the season?
"You've got to ask yourself, can they change it at a Council of Clubs meeting, without going back and changing the constitution?
"If the rule had been in that year we still wouldn't have won the Weekes Cup in 2011, and we had two teams in the finals."
The matter will pour out again at the next Council of Clubs meeting on February 12, with the prospect of an affirming or rescinding vote.
Neither the Border nor Ratana club delegates were at the December meeting.
Marist are standing their ground on the rule change. "Why should we be disadvantaged when we've gone out and got these teams?" said club secretary Clark Allan.
"We don't know how it got changed when all of the points got done on your top points scorer [in senior].
"We were always against that."
Marist, working hard to build up their player base, benefited Wanganui rugby - in extra fees paid to the union as well as the extra money received from the New Zealand Rugby Union for more registered players, Allan said.
Marist's two senior teams started training this week.
"You never know with these Senior Bs, who show up maybe three to four weeks before the season," said Allan.
"It could very well happen we might not have another team. But our coaches are confident."
There are split views across the city and country clubs.
Both Taihape and Utiku voted against the motion and their spokesmen backed Ruapehu's stand, although those clubs are unlikely to follow suit and withdraw from cup contention.
Meanwhile, Kaierau and 2012 Weekes Cup holders Pirates have no problem with the rule change.
"Good on Marist for having two teams in that grade, but I still think it's an unfair advantage," said Utiku's council delegate Sean Kelly.
"All of a sudden, they've changed the rules.
"We support where [Ruapehu's] coming from.
"We do struggle to put two [teams] out. It is a battle for country."
Pirates chairman Nga Apai said the format was "bang on".
"Having to say Marist is a one-horse race, I don't take that stance.
"The only way that happens is if both their senior teams make the semifinals. If your teams make the semifinals, fair enough.
"It's all about who is developing the strength of their club."
Kaierau president Geoff Davies said they might ask for their under-19 team to be taken into consideration.
The rule would be, in effect, for any club which grew its player base for more teams, he said.
"In a couple of years' time, it could be us, it could be Pirates, it could be any club.
"You've got to look at the big picture."
John Phillips, club liaison officer for the WRFU, said he was "very surprised" the motion got through, the third year Marist had tried.
"That will now be debated under general business at the next Council of Clubs meeting.
"It could be taken to a vote and that previous motion rescinded."
Phillips said it had never happened before in Wanganui rugby that a club has refused to contest a championship.
"It will be unprecedented and Ruapehu have won that trophy for a few years now.
"It will bring it to a head."
