The tourist attraction off, the A5 south of Oswestry, had put forward plans for its future, along with its request for retrospective permission for buildings put up without planning consent.
The family-owned business, which has now withdrawn the proposal, said it had been advised to submit a new application purely concerning the retrospective permission.
Chairman of the centre, Clive Knowles, blames commercial conflict for scuppering his plans to develop the site further, at least in the short term.
He says objections from rival businesses have coincided with the demise of the application and has called for planners to be more robust in dealing with what he calls vexatious objections.
"After two-and-a-half years of putting these plans together we are in despair that we have been frustrated by the planning process and that we are having to go back to the drawing board and submit a new application," he said.
"We have spend tens of thousands of pounds commissioning reports that were called for by the authority and now we have been advised to start again from scratch.
"We are held in very high esteem and are the fourth most popular tourist attraction in Shropshire on Trip Advisor despite having no public funding for what we do. We have had hundreds of letters of support and we feel that the tourist industry in Shropshire has been let down."
Mr Knowles said his disappointment was that many of the plans would now not go forward in the short term.
"We were in talks with the National Cycle Museum to return it from Mid Wales to Oswestry where it was first created. We cannot go forward with those and it means letting a wonderful project down.
"Our nature reserve cannot go ahead and plans for our train to take people, including those with mobility problems, around the centre and its station have been derailed."
"We had great plans for a dedicated building to house a Shropshire Youth Trust hub that recently opened here. That is now all up in the air."
Mr Knowles said his family's first priority is to its staff and re-assuring them about the future.
"We want to reassure them that we will find a way to move forward," he said.
A new planning application for the buildings currently at the Ironwork Centre and an improved access from the A5 will now be drawn up for submission to Shropshire Council.