It said there were already a number of unfilled vacancies at the agency, with little or no indication that they would be filled.
The union accused the Government of claiming that not filling jobs when people left through early retirement and voluntary redundancy or not filling vacant posts, did not seem to count as a job loss.
The union maintained there would be 3,000 fewer people working for the Environment Agency in three years time than there were 18 months ago.
GMB general secretary Paul Kenny said: "These are job losses pure and simple as they are posts which will not available to young workers or others seeking work."
An Environment Agency spokesperson said the GMB had done simplistic maths based on budget settlements and added: "We do not recognise the figure that has been quoted."