Officials from the Scottish Environmental Protection Agency (Sepa), the Scottish Government and the Forestry Commission have now ordered that no more sewage should be brought onto the farm leased by tenant farmer Alister Orr.
After a crisis meeting at Carserigg, by Kelloholm in Dumfries and Galloway, Mr Orr was also told to clear up or remove some of the matter to prevent contamination of nearby streams.
An inquiry into the use of the sludge by Mr Orr, who was selected by the Scottish Government's flagship "new entrant" scheme that backs recruits to the agricultural industry, is now under way.
The use of human sewage to restore hard-to-farm land is permitted by licence under strict regulations, but concerns have been raised over the way the sewage was applied.
Jim Walker, past president of the National Farmers Union Scotland, farms near to Mr Orr and started to notice a bad smell in the area more than two weeks ago. He said: "I went out to investigate and I couldn't believe it. Spreaders, lorries and skips … and human sewage spread across grass fields. You are meant to plough it in immediately but this was just lying on the surface.
"If this stuff is treated with lime to ensure there are no pathogens left, such as E. coli, then it's fine. But here you had maggots, bluebottles and flies. There are pools of human sewage. It's lying in piles and it is on the roads.
"This is a licence to dump 10,000 ton of human waste on fields in Dumfries; and Sepa, nor anyone, thought it appropriate to notify or consult on this with the local villages and neighbours. Its obscene. I don't know why anybody in their right mind would think this was OK to do."
Licences to use sewage sludge are typically granted to boost the soil content of former industrial sites, with Sepa granting permission in this case given the farm sits over an former open-cast mine.
However, it has been claimed the land being treated by Mr Orr is pasture, with the site not used as a mine for around 20 years.
Sepa said, following complaints, it was satisfied the waste had been treated and applied properly, with inspectors not observing any environmental harm. However, a spokesman added that no more material will be brought onto the site at this time as an investigation was under way.
The spokesman said: "To date, Sepa has not observed any impact on the local environment as a result of sewerage sludge being used; however, we will continue to liaise with both the Forestry Commission Scotland and Rural Payments and Inspections Directorate with regards the regulation of this site."
A Forestry Commission spokesman said some work will take place at Carserigg to "properly" finish the operation. He added: "A thorough investigation into the sludge operation is to be carried out to determine if all the regulations have been adhered to."
A holding place for the sewage, which was brought onto the site by a Kilmarnock-based company, will be dismantled.
Councillor John Syme (Labour) of Mid Upper Nitsdale ward, said: "I am not very comfortable with it at all. Apart from the smell, I worry whether this is going to finish up in the rivers or in the fields where the kids are playing. We should not be in a situation where there are human faeces visible in the fields."
Mr Orr declined to comment.