A Flood risk assessment is being called for by the Environment Agency to determine what impact a new community medical centre would have on Upton.
Plans for the building at the bottom of Tunnel Hill were submitted last week by doctors at the town's School Lane surgery.
The development has been on the drawing board since July 2001 but was delayed by Environment Agency fears that it could worsen local flooding.
David Murray, head of development control at Malvern Hills District Council, said last week that he believed the concerns had been dealt with by locating all of the building above the flood plain. However, the Environment Agency is still worried.
Spokesman Oliver Blackburn, said that while the medical centre was outside the 100-year flood level, the car park would encroach on it.
"In general, it means less of the area where flood waters can go," he said.
The issues that the Environment Agency is recommending for examination are the importance of flood flow by the site, the loss of storage for flood water, the environmental risk posed by cars and the development during flooding and the potential impact downstream of the site should a flood occur.
Mr Murray said if the Environment Agency continued to object after a risk assessment, then planning officers would recommend refusal of the application.
"The likelihood is that the objection is capable of being resolved," he said. "If that risk is a low one, it's possible the Environment Agency will withdraw its objection."
Although the agency's comments are taken into account by planners, the final decision lies with the district council and will be made over the coming weeks.
Peter Icke, of site architects Gould Singleton Partnership, dismissed the concerns listed by the Environment Agency.
He said: "We're not outwardly affecting the current status quo. I'm confident we can overcome these issues."
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