Property Alliance Group is to appeal after its application for a £40m scheme aimed at revitalising Radcliffe in Bury was rejected.
The group submitted plans to build 310 house and apartments, 73,000 sq ft of light industrial units, and 12,000 sq ft of office space on the 28-acre Dumers Lane site.
But the application was turned down by members of the council's planning control committee who voted ten to one against it.
The land, formerly used by the Halls sweet manufacturer, has been earmarked solely as an employment regeneration area which the council is is keen to preserve to create new jobs in the future.
In order to make the £21m project financially viable, the group wanted to turn 50% of the site into housing, with the other 50% being split into office space and river widening to protect against flooding.
That meant that only 25% of the site could be used for employment purposes.
In order to satisfy the council's demands for employment space, Alliance had planned to plough a further £18m into the Chamber Hall site on Carlisle Street in a linked scheme – even when it emerged that that had also turned into a flood risk zone – in order to provide a further 90,000 sq ft of offices.
But the council's rejection of the Dumers Lane site means the group is no longer prepared to invest in Carlisle Street alone.
Lee Charnley, a director of the company, said: "We will appeal against this decision in the new year.
David Russell, chairman of Property Alliance Group, added: "Our basic and easily understood argument is that the site lies entirely within the Environment Agency defined flood plain.
"It will take many millions of pounds to raise the site levels and widen the river corridor to take the site, and adjoining houses, out of the flood risk zone. Industrial development alone will show a developer's loss – therefore, and logically, a 100 per cent industrial development will never happen.
"It is therefore absolutely essential that residential development is permitted on part of the site so as to generate the necessary cross-subsidisation to enable the flood mitigation works to be carried out and employment to be created on the site.
"Not one councillor at the meeting even commented upon this fundamental viability argument, even though the evidence was relayed at the planning meeting and more comprehensively within the planning application documents."
Alliance has previously intimated it would build a prison on the site if their proposal for the former Halls site was refused planning permission and is still prepared to consider it as an option should their appeal also be rejected.