Farmers say the 2019 Budget has left a critical gap in the Government's commitment to conservation.
Federated Farmers said in a statement there was no additional funding for the QEII National Trust or the Ngā Whenua Rāhui Fund.
Arable and biosecurity spokeswoman Karen Williams said there was also "woefully inadequate" funding for the control of wilding conifers.
She said the "extremely modest" increase in funding for the National Wilding Conifer Control Programme meant its work would be going backwards in terms of managing the pest.
"We hoped to see the wilding conifer programme receive more like $25 million per year.
"It's a $250 million problem growing at 20 per cent per year. We are not even going to hold our own at $10 million.
"By ignoring the problem all the Government is doing is pushing the responsibility further down the line for someone else to fix. If the country is not going to take pest plant wilding conifers seriously then it's about time it was just said out loud."
Federated Farmers said QEII and the Department of Conservation's Ngā Whenua Rāhui funded covenants provided the most cost effective and secure method of protecting and enhancing biodiversity values on private land.
Federated Farmers had worked closely with other non-government organisations and the Government on developing a workable National Biodiversity Strategy as part of the Biodiversity Collaborative Group.
This group had identified the benefits of supporting the protection of indigenous biodiversity on private and Māori-owned land respectively.
The demand for new covenants had outstripped demand.
"The Crown and the public expect greater protection of biodiversity value on private land to occur. How can work continue if the Government is not prepared to help fund it?"
QEII covenants protected more than 180,000 hectares on private land and played a critical role as a refuge for some of New Zealand's rarest and most endangered ecosystems.
"It's unfortunate the Government can't see its way to support conservation efforts with a tried and true track record."