That involved covenantors receiving the same amount of support for the next three years by way of automatic grants credited to their rates accounts, before a regional grants scheme would take effect.
The council had allocated $200,000 from the 2019/2020 year to enable the new scheme, which council officers would work with the trust to develop.
But the trust said its members would be "deeply disappointed" at that outcome, and argued the grants should be awarded on top of rates remissions.
Covenant holders made a significant contribution to conservation by protecting their land forever, but the trust was worried the move could put others off joining them.
"Auckland Council has its priorities wrong with this new policy and we intend to fight it, and we are leaving all options on the table at this time," trust chief executive Mike Jebson said.
Legal action was one possibility, Jebson said, along with going to the Government.
The trust was also unhappy with the way the council had proposed and consulted on the changes, calling the process "shambolic from the start".
"We had to lobby to ensure that all affected parties were consulted on this policy, and they made a decision on 31 May, yet only notified affected parties this morning," he said.
"They asked for submissions but have ignored the majority of submitters who were against the removal of rates remission for protected land."
Jebson said the trust had been "flooded with calls and emails" from Auckland members.
The trust ultimately believed QEII covenanted land was automatically non-rateable under the Local Government (Rating) Act 2002 - and the council charging rates on QEII land was contrary to the law.
"We don't have a choice but to fight this policy on behalf of our members and covenantors, recognising the contribution these land owners make is the right thing to do on behalf of all New Zealanders."
Auckland Council financial policy manager Andrew Duncan said the changes were adopted because the current rates remission policies for land with QEII covenants were carried over from the legacy councils, and were "not equitable" Auckland-wide.
"For example, the level of remission grants up to 100 per cent of rates for QEII covenanted land in Auckland City, Franklin, Papakura and Rodney Local Board areas, but only 10 per cent in other areas," he said.
"A robust consultation process was held prior to taking the proposal to the F&P Committee, and the final policy included amendments reflecting this.
"It also worth noting that 17 of the 21 local boards supported the proposal in full.
"Furthermore, we appreciate the feedback from the QEII National Trust and look forward to continuing to work with them closely."
