Policy officers have recommended planning permission be refused for affordable homes on the former Lucent Technology site.
The Minton Group, which specialises in leasing office, industrial and warehouse space, has been looking for a buyer for the site on the Swindon Road since April last year.
The company came up with an ambitious scheme to boost the number of people working from home.
They proposed to build one to four- bedroom houses with office space on a separate floor or adjacent to the house.
Affordable housing was also to be included in the scheme with a restaurant and nursery.
But council officers have rejected the project because the proposed development is in the countryside, outside their framework boundary where residential development is unacceptable.
They also argue the plan would lose too much land that could be used for future employment.
The problems have been compounded by the lack of information among local people on the project.
Landlord of the Rose and Crown pub in Malmesbury, Tony Mantle, said people needed more information.
Mr Mantle said: "I see no harm in putting a derelict building to good use, but it is all very nebulous and we do not know enough."
Malmesbury and St Paul Without parish councillor Daphne Jones said members felt the proposed redevelopment was generally a good idea.
Mrs Jones said: "Our general impression is that this is an interesting and enterprising idea. We support the application but are worried about safety issues associated with the river and potential access by children."
District and county councillor John Thompson said he needed more information before making a decision.
Mr Thompson said: "There are a lot of unanswered questions here. We do not really know what is the demand for affordable homes and I do not want to lose the employment site."
North Wiltshire District Council will now consider the proposal at a development control committee on September 1 at 7pm.
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