One academy staff member said that a new single internet portal for the centres was "clumsy, unwieldy and not fit for purpose".
The HEA's 24 subject centres were established to provide teaching support to academics and share best practice, and each has had its own independent website. Since a 2005 feasibility study, eight subject centres have been involved in a pilot aimed at setting up a single portal, but there is serious discontent.
Norton Miller, the web development officer at HEA's Subject Centre for History, Classics and Archaeology, is being made redundant after six years in the job. He agreed to speak out, while others have remained anonymous.
He said the HEA had "panic bought" the wrong system, towards the end of a financial year, and it had cost between £150,000 and £200,000.
"It's not fit for purpose. It's clumsy, it's unwieldy ... and it doesn't deliver the functionality that we need as a centre, and we all need collectively," he said.
A second member of staff called the project a "mammoth waste of money", said it was "on the verge of collapse" and complained of "long-winded and complicated" maintenance.
A third added: "If all the technical people from the subject centres got together, I'm sure we could easily have built a much better system that works."
Sean Mackney, deputy chief executive of the HEA, declined to confirm the cost of the project.
He said the move to a centralised website would improve on the current "fragmented" offering, and he denied that the academy had been rushed into buying the wrong system. He said the HEA had commissioned a study of users and chosen a package "appropriately".
"Speaking to subject centre directors, there (are) a range of views about the next phase of the project," he said.
"One of the important things to learn from the pilot is the need to support technical colleagues, to help them make use of the system that we've got."