In a statement, campaign group Fish Legal and the Gwent Angling Society said they sent a "formal complaint" to the Brecon Beacons National Park Authority (BBNPA) stating that the digester, which is operated by family run company GP Biotec at Great Porthamel Farm near Brecon, has been operating without planning consent.
According to Fish Legal, this includes its lagoons and slurry tanks located on the banks of the river Llynfi, a site of special scientific interest and a tributary of the river Wye special area of conservation.
A retrospective planning application for the "retention of digestate stores" at the site was submitted to BBNPA last month.
A statement from Fish Legal said that, in "order to rectify the ongoing planning breaches, BBNPA has invited the operator of [the site] to make a retrospective planning application to cover all its operations currently taking place without planning consent".
The digester was at the centre of a failed legal challenge against the decision by Powys County Council to grant planning permission for additional intensive poultry units at a site at Builth Wells last year.
There was an agreement in place between the poultry producers and GP Biotec that its plant at Great Porthamel Farm would accept the manure and dirty water generated from the increased poultry production arising from the consent.
Penelope Gane, head of practice at Fish Legal, said: "It is extraordinary that [BBNPA] is allowing this facility to continue operating when not all of its structures are legal."
"We are not talking about a kitchen extension here. This is a huge industrial site processing tens of thousands of tonnes of manure and slurry every year in the Wye catchment."
Dave Collins, vice chair of Gwent Angling Society, which leases one Llynfi fishery, claimed that crucial documents relating to drainage plans for the plant had not yet been given to the BBNPA for use in its consideration of the retrospective application.
He also claimed the authority had "repeatedly missed opportunities" to take action which he said had allowed the company to continue with "virtual immunity".
He added: "Over the last seven years, in spite of the repeated loss of angling amenity, we have invested significant time and resources into the lower river's recovery. But we live in fear of the next phone call with news of another fish kill, once more destroying our fisheries and the river habitat. Action to stop this site being a pollution risk should be a top priority for the authorities."
GP Biotec and BBNPA have been contacted for a comment.