A special meeting was held before the trust's annual meeting on Thursday night to discuss and vote on the proposed changes which included creating the ability to appoint three members to the six-member elected board.
The issue drew 7% of the trust's members, about 85 people, twice the usual turnout for an annual meeting.
Trust chairman Neville Peat said a secret ballot was held at the request of two members, with 42 in favour and 37 against.
"It wasn't a large majority. It signalled to me that, one, we probably need better explanation of the implications of the expanded board."
There was some unease from members about who would get appointed and if all three of the appointed members could be from Kati Huirapa Runaka ki Puketeraki.
However, Mr Peat said that was not the case as it was set out clearly in the new deed that it would be "a representative" and they would be accompanied by a memorandum of understanding setting out the relationship between the two organisations.
Mr Peat said he had never felt any undue pressure from the runaka.
"The changes are not a threat; they are a strengthening of our ability."
It would be next year, at the earliest, before the board considered "who to invite, if anyone" and it was working on a memorandum of understanding.
Former chairman and Orokonui founder Dr Ralph Allen, who opposed the changes, said the decision to proceed with the rule change was arrived at democratically.
"However, with just six votes deciding the outcome, I don't think it represents a ringing endorsement of the trust board's objectives."
Trust members had put the board and the runaka on notice to prove that the interests of wildlife had priority over other considerations, he said.
"How they proceed over the next 12 months will demonstrate their commitment to that."
New trustees elected to the board were Dr Kelvin Lloyd, one of the founding trustees, and replacing Stuart Harvey, who had retired from the trust, was Ross Smith, the retired chief executive of WHK.
