Henry Elliot, chairman of the Royal Zoological Society of Scotland's Council of Trustees, said the council's move was "ill-considered" and would have a "profound impact" on the zoo.
The zoo wants to sell greenbelt land off Kaimes Road to housebuilders to help fund its 72 million masterplan.
But the planning committee of the SNP/Lib Dem-led council has overturned the old council's support for the plan.
The council intends to side with local protesters, who have raised fears about severe congestion on local roads, at a public inquiry which will consider the issue next year.
Mr Elliot has now spoken out following a meeting of the trustees which considered the council's latest move.
"We will be looking at whether a way can be found to reverse this ill-considered planning decision so that the Society can continue to fulfil its vital wider role," he said.
"The planning committee's decision feels, personally, like a kick in the guts and, for the Society, like a rejection of all we stand for. I am deeply disappointed.
"Conservation and the environment are now matters of intense public interest and we are all urged by governments, local and national, to take action.
"Yet, apparently for local reasons, this decision may have a profound impact on an organisation that is actively engaged with these very issues.
"The work we do in conservation, research and education is incredibly important, and our increasing membership and growing number of visitors over the past few years show that the public support us."
The zoo has grown to become the second most popular paid tourist attraction in Scotland, with more than 650,000 visitors a year.
Any profit made from housing developments would be channelled back into the zoo's masterplan, which aims to make it one of the best in the world and which would have the potential to bring in an estimated 1 billion to the local economy over 20 years.
Local councillor Paul Edie said: "I am disappointed that the zoo is going to continue to press for these plans, but not surprised.
"The decision we made was hugely important as now we will go into the public inquiry with the full backing of the council to oppose these plans.
"I have a lot of sympathy with the zoo. My first summer job was working at the zoo, so I appreciate the importance of their modernisation. But I feel that these are very badly thought-out plans, and in my opinion the zoo should seek to modernise on the land it has."
Councillor Lesley Hinds, a member of the planning committee, said:
"Obviously, there were a number of objections from the local area, but I think there was a strong case from the zoo.
"This looks certain to be discussed at a public inquiry and I think that is probably for the best as it will give both the zoo and the objectors a chance to put forward their arguments."