Doughty led English Nature from 2001 to 2006 and continued after it merged with other agencies to become Natural England.
He worked at Derbyshire County Council for 20 years. From 1993 to 2002, he was chairman of the Peak District National Parks Authority. He was knighted in 2004.
Defra secretary Hilary Benn said: "Martin was an outstanding public servant and his loss will be deeply felt by all those who knew him. He founded and led Natural England with distinction and was passionate in his advocacy of the natural world."