Councillors Bruce Gordon and John Turkington voted against it - both are from Rangitīkei.
They were joined by Horowhenua councillor Sam Ferguson, who said the work the groups do is needed and they haven't been spoken to about the funding change.
"We have put at risk the ability for them to achieve these outcomes. We are ripping the rug out from under them."
The council's draft Long Term Plan proposes funding all community biodiversity projects from a pool of $260,000. The groups will have to apply for funding, in a new process.
If REG makes a successful application, its work will be funded by the whole region rather than by Rangitīkei ratepayers.
Old man's beard is a scary and growing problem. The Rangitīkei District is considered a containment zone for it, and Horizons does little work there to control it, Gordon said.
"In effect this is just a breeding ground.
"We have never had enough money and the old man's beard problem is getting bigger and bigger.
"The biodiversity jewels in our crown are literally dying before our eyes."
REG has some new money from the Rangitīkei River Catchment Collective, to combat the weed on private land. It could allow the group to have three teams working year-round, rather than its current two teams working during the summer months only.
There is no guarantee that money will last. If the Horizons funding disappears REG could find itself working only on private land, Gordon said.
"It would mean that all the public-good stuff would effectively disappear."
He was relieved to hear the Long Term Plan will be open for submissions, and said REG would submit to keep its funding.
Councillors who voted to make funding for the two groups contestable said it put all the biodiversity projects on a level playing field. Each can apply to the council for targeted rates in their regions, and their supporters can submit to the Long Term Plan.
"If these projects are as awesome as everybody says, they will get funding," David Cotton said.
The draft Long Term Plan proposes only five "iconic" projects will receive guaranteed funding for one to three years. They include Kia Wharite in the middle reaches of the Whanganui River and Pukaha Mount Bruce in the Wairarapa. All focus on complete habitats, Horizons chairwoman Rachel Keedwell said.
The funding change was suggested by Nicola Patrick.
"This means we are truly prioritising the most important work on the basis of the science we are receiving," she said.