Daws Hall reserve is a haven for otters and nesting birds
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Network Rail has been threatened with court action after hundreds of yards of hedgerows near train tracks in Essex were cut down.
The company says it was trying to improve visibility for drivers on the line between Sudbury and Marks Tey, which crosses Daws Hall reserve.
Reserve Trustee Major Iain Grahame said contractors have disturbed nesting birds and this was illegal.
Network Rail has denied the allegations and said the work was essential.
Mr Grahame said some of the most threatened animals in East Anglia - such as otters which live on the reserve - had only just begun to make a comeback before work started.
'Safety reasons'
"Yesterday (Thursday) I found these people felling trees within five yards of a otter hole which I know has been in recent use"
Network Rail's Chris Rumfitt said a number of drivers had complained of poor visibility and speed restrictions had been imposed.
"For safety reasons and to improve passenger service we've got to do this work now.
"We have ecologists assessing our work and we're not chopping down trees with nesting birds in them."
Mr Grahame has met the contractors and accepts that visibility must be improved but does not accept the work should be carried out right now.