Moving 55 water voles from the Somerset Levels ahead of dredging work cost £24,000, it has been revealed.
About 130,000 cubic metres of silt was removed from the rivers Parrett and Tone at Burrowbridge, last year.
To complete the work, the Environment Agency (EA) said a "substantial relocation project" costing around £436 per vole had to be carried out.
An EA spokesman said: "We had a legal duty to move the voles, which are critically endangered and protected."
As part of an £86,000 wildlife survey, the voles were trapped along a five mile (8km) stretch of the two rivers.
But moving the animals to an "over-wintering facility" and relocating them to Hampshire and Cornwall cost an additional £24,000, the agency said.
'Unusual for agency'
"The over-wintering is necessary to ensure their survival," an EA spokesman said.
"Relocating them was an essential piece of work - if we hadn't moved this population of voles then it would not have been possible to complete the dredging.
"It is unusual for the agency to undertake a substantial relocation project like this."
Large parts of the Somerset Levels spent much of the winter of 2013-14 under water.
The dredging formed the first phase of the 20-year Somerset Flood Action Plan.