Earthwork repairs on the Cononley washlands, near Skipton, have been cancelled because of the foot and mouth epidemic.
Environment Agency staff have been unable to reach the area - designed to hold millions of gallons of water during heavy flooding - which is in an infected area.
David Wilkes, the EA Ridings area flood defence and water resources manager, said it meant water could overflow from the River Aire into the washlands earlier than expected in a flood. He told the Yorkshire Regional Flood Defence Committee in Leeds that the floods in October and November last year had left some defences in a state of disrepair.
About 350 people fled their homes in the Stockbridge area of Keighley last October when the River Aire burst its banks and engulfed houses. The floods also destroyed the Yorkshire Dales Ice Cream factory at Cononley forcing it to move its production elsewhere costing about 50 jobs.
"Repairs are required within the Skipton and Cononley washlands and these will not be completed this year, since they lie within the infected area," said Mr Wilkes.
"The works include small earth banking repairs and foreshore erosion, meaning the washlands may operate prematurely in a flood."
The aim was to carry out the work once the restrictions were lifted and he stressed that meanwhile there was no increased risk of flooding further down the valley.
Regionally there is a need to spend £350 million over the next ten years on capital schemes, flood warning schemes and maintenance.
"This is a serious number of homes under threat. Protecting them is about protecting the economic and social health of the region," said Mr Wilkes.
"We are giving the best protection we can, but our annual expenditure is about £27 million and the average potential flood damage figure is ten times that at £270 million," he added.
The flood defence committee agreed to hold a meeting on December 7 to agree prioritising funding options.
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