A number of houses were broken into early on Monday, officers said.
Goods left outside affected homes in the Calderdale of West Yorkshire were also stolen, it emerged.
"It is impossible to comprehend why anyone would want to bring further suffering to those already in a very vulnerable situation," said acting Supt Mark Grange, of North Yorkshire Police.
Houses in Huntingdon Road, York, were targeted after the River Foss broke its banks, with one being looted after the back door was forced, as well as tools being taken from a shed at another property.
West Yorkshire Police said it had received reports of people using white vans to take "dry goods left outside flooded homes", in the Calderdale area.
No arrests have been made in connection with the thefts and burglaries, which emerged after the levels of the Foss dropped by several metres on Tuesday.
Six severe flood warnings, in place since Boxing Day, were lifted by the Environment Agency, which said emergency repairs to the Foss Barrier had allowed four of eight pumps to begin working again.
Areas across northern England however, are braced for further disruption as Storm Frank, which hit the UK late on Tuesday, brings in more high winds and heavy rain.
Looters who targeted flood victims' homes in York have been condemned by police.