The UFU president rejected the claimed that the union was trying to dictate Daera policies.
“This organisation has 120 years of history”, McLenaghan told the BBC’s Good Morning Ulster programme.
“It has worked with every government there has been, every competent authority there has been – whethers it’s Westminster or Stormont.
“Any political party that has held the ministry, we’ve worked with them to help them, to help our farmers, to help our industry.
“To describe that as dictating is not only unfair on the Ulster Farmers’ Union, it’s also actually somewhat disingenuous.”
McLenaghan pointed out that the UFU is often invited to with Daera on “co-design” projects because of staffing and resources issues within the department.
The UFU president insisted that the call for Muir to quit was made after the terms of reference of the review into the Fivemiletown cull.
The process is to be led by Dr Martin Blake, a former Chief Veterinary Officer for Ireland and is expected to report by early autumn.
“We were always clear that in order for this review to be thorough, to get the answers that we need, it needed to be more than just purely an analysis of ‘did the vets follow procedure?’ McLenaghan said.
“It needed to look into the legalities of the process and also take consideration of both animal and farmer welfare… that we didn’t get.”
Warning: This article contains an image of dead animals that some may find distressing
Speaking on the same programme, Alliance Deputy leader Eóin Tennyson claimed the cull was being used as an excuse to target Muir’s job.
“The fact that the UFU have called for a resignation before that review has even concluded, I think speaks very plainly to the motivations behind this,” he said.
“They are not concerned about the case at Fivemiletown or animal welfare issues, as they profess.
“They are concerned about the fact that for the first time in the history of the Northern Ireland Executive we have a minister who is not beholden to vested interest.”
Tennyson argued the review needed to be carried out quickly and if Muir was to appoint a larger panel of experts that would delay the outcome of the process.
But McLenaghan said if there were three people on the panel, like the UFU had requested, they could “share the workload” and it could be completed faster.
