SEPA issued the notice to the operators of the Dargavel plant.
It was issued to the firm last Friday and comes into effect on 23 September.
The agency cited four reasons for the notice. They are:
- Persistent non-compliance with the requirements of the permit
- Failure to comply with an enforcement notice
- Failure to maintain financial provision and resources to comply with the requirements of the permit
- Failure to recover energy with a high level of efficiency.
In addition to the permit, SEPA is looking to avoid pollution and return the site to a "satisfactory state".
This includes a requirement for the waste at the site to be removed.
Scotgen (Dumfries) Limited is entitled to appeal to the Scottish Ministers against the notice.
If an appeal is made, the revocation notice would be set aside until the appeal has been determined. This would mean the plant could carry on operating until the Scottish Minister make a decision.
Ian Conroy, SEPA's Technical Support Manager in the South West, said: "SEPA recognises the importance of plants like this as part of the overall mix of facilities and services that will have a role in delivering a Zero Waste Scotland.
"Since the plant come into operation we have provided support and assistance to Scotgen (Dumfries) Limited including affording them considerable time and opportunity to demonstrate that this facility can meet the Best Available Techniques, and the specific requirements of European Directives designed to protect the environment.
"Unfortunately despite this, they have not done so. The facility started operations more than four years ago, and in that time has never achieved a level of compliance which would give SEPA any degree of confidence that future operation would be any different. The facility has consistently failed to meet any reasonable expectation of environmental performance and the predicted level of energy recovery at approximately 3% is particularly disappointing and unsatisfactory.
"SEPA has taken this serious and unusual action of revoking the permit following careful consideration and assessment of the regulatory options available."
It is understood Scotgen is currently considering its options with advisers.
Last month, a major blaze broke out at the £20m site. More than 30 firefighters were dispatched to deal with the fire.
(JP/CD)