The 53-year-old is being treated in the high dependency unit at Ninewells Hospital, Dundee for severe damage to his lungs.
It is thought that his symptoms may have been caused by gas inhalation- possibly hydrogen sulphide- from rotting carcasses.
Exposure to hydrogen sulphide causes lung and eye irritation and breathlessness and can be fatal in high doses.
Police told the Scotland Courier that three other employees were being treated for irritation to their lungs.
"For some reason there appears to have been a build-up of hydrogen sulphide in the area of the rendering plant and two employees were overcome with the fumes when they went in to dump another load of animal material," said Inspector Donald Thomson.
"A third employee was affected when he went to render assistance."
The plant, Sacone Environmental Ltd, was evacuated as a precaution and has now been closed down.
The Health and Safety Executive has launched an investigation into the incident.
It has been revealed that the Scottish Environmental Protection Agency (SEPA) has served three enforcement orders on the facility- which burns the animal carcases- over the past year.
A statement released to local press by the company said work would not resume at the plant until it was considered safe and stressed that management at the plant were co-operating fully with the authorities.