The Daily Telegraph claims agency officials met with Network Rail last month, saying plans to protect the train line at Dawlish were put off so the impact it would have on birds could be looked at.
The track was severely damaged by storms this week.
A spokesperson for the Environment Agency says they "do not recognise the description" of the meeting.
Exeter leisure centre to get revamp
'This is a fantastic opportunity for our area'
£400k plans for extension of heritage railway line
Team want to get it all the way to Bideford
Chiefs see off Sale in thrilling encounter
Exeter move into the top 4
Plans to change Torbay heart care dropped
Victory for campaigners
Torbay taxi driver stripped of licence after making video call
Driver carried passengers in untaxed vehicle
Row amplifies after public claims edited out
Comments made by a resident have been removed
