Rushmoor Council has accused developer Barratt Southern Counties of abusing the process by trying to amend its plans to build 139 homes then appealing to the Planning Inspectorate just three days later.
But in response to the borough's refusal to accept the amendments, Barratt claims it is not being treated fairly.
The developer has submitted two identical applications to build an estate on the old Farnborough College of Technology annexe site.
In such cases, if permission is refused a developer can appeal on one application while negotiating the other with the council — a practice known at "twin-tracking" which is under review in the government's planning Green Paper.
Rushmoor's development control committee believes Barratt is acting unreasonably.
"They're playing both ends against the middle," said chairman Cllr John Debenham.
"They want their appeal and they want to negotiate. As far as I am concerned it's one or the other. They're not negotiating if they're appealing."
Director of planning Keith Holland said the council was not obliged to accept the amended plans.
He added: "We're considering them on the basis of their original plans. We did not have time to consider the amendments before the appeal was lodged three days later."
Though the changes proposed did not alter the design or number of homes in the application, Mr Holland said the layout was fundamentally different. "It's something we would have wished to consult people with," he added.
He said he would strongly recommend the Inspectorate to consider the original plans in the appeal but could not rule against the developer presenting the amendments.
Barratt spokesman Robert Barlow said it was doing nothing wrong: "We consulted with planners and local people, taking on board the things which are contentious and the planning policy point of view.
"We've adjusted the plan to take in many points and now they're telling us they're refusing to consider the original one because of the appeal."
He said the company wanted to meet Rushmoor chief executive Andrew Lloyd as it is not convinced the council's behaviour is legitimate.
He said the amendments involved minor detailed changes and were in keeping with local planning policies.
Barratt was also criticised for the fence it put up after gaining permission to demolish the former college building.
Local councillor and deputy mayor George Paparesti said residents had complained: "They're asking: ‘Why do we have to have such a high fence?' Many fear Barratt has something to hide — that's what's coming across."
Cabinet member David Clifford added: "It looks like something out of communist eastern Europe. It really beggars belief what's going through their minds."
A resident put a message on it: "The Berlin Wall by Barratts".