There is particular concern that the current waste collection permit system for slurry and sewage is not functioning. Under waste legislation from June 2002, all contractors moving slurry or sludge for profit must have permits.
However farmers moving slurry from one part of their land to another are exempt.
Figures obtained by The Irish Times show only nine contractors in the north-east region, nine in Cork, two in Donegal and 15 in the mid-west are authorised to move slurry or sludge. Local authority officials admit that there must be more contractors needing permits.
Ms Christina Sullivan, environmental science officer with Galway County Council, said on the agricultural side there were probably quite a few operating without a permit.
Mr Tony Waldron, who with the Carra-Mask Water Protection Group Ltd has lobbied the European Commission over Ireland's poor water protection, has described the system as a "farce".
Mr Jim Devlin, of the IFA, said the reason there were not many permits for moving slurry was that manures and slurry was recovered on the lands on which they originated. As only people moving material from one place to another for reward needed a permit, it was not relevant to normal farming.
However, Ms Katherine Walsh, head of environment at Cork County Council, said it was known there were contractors working for reward without permits.
Only 10 of 118 contractors which were contacted by the council in May 2002 have applied for a permit.
Limited resources are another reason local authorities say they have not been focusing on authorising the movement of slurry and sludge. Mr Cyril Morris, co-ordinator of the mid-west regional waste authority, said collection permits were only a very small part of its work.
The Minister for the Environment, Mr Cullen, has defended the small number of permitted contractors, saying slurries/manure was the last waste category brought within the system.