The body charged with protecting Scotland’s environment is to allow factories, public utilities and even nuclear power stations to monitor their own discharges.

The move to allow the bodies that come under the control of the Scottish Environment Protection Agency (Sepa) to carry out their own tests has sparked concern with an MPS vowing to raise the issue with ministers.

Sepa is to implement its new Regulatory Evidence Strategy over the next two years, and according to a leaked internal email “this will have substantial implications for Sepa".

This memo explains: “It means that operators (including Scottish Water) have to monitor their own assets and report the results to us and the public. We have to set-up processes to audit them and make sure they are complying.”

It says it will release resources to collect a wider range of new information to inform Sepa’s decisions, and continues: “This was a big decision for Sepa and one we have thought very carefully about over the last 18 months.

"We are convinced that this change will substantially increase our ability to protect and improve the environment, and target our resources to where they can make the greatest difference.”

But the scientist who leaked the memo, who has long experience within Sepa, insisted: “The agency is effectively abandoning it is own direct sampling and analysis, for example, where a river is receiving effluent from a manufacturing plant. Instead it will rely on monitoring the operators’ results, only verifying that the sampling from the river has been done properly.

“This implication for waste is also particularly concerning given a few operators may try to dispose of hazardous waste as normal waste, which would have huge financial benefits for them. I am also aware that Scottish Water already pays their managers bonuses partly for meeting Sepa targets, given that they are the biggest discharger in Scotland and that they also likely to carry out their own chemical analysis of the samples, can self-monitoring be right there? Look at lack of confidence angling interests have in fish-farms which already undertake self-monitoring.”

However Martin Marsden, Sepa’s head of environmental quality said: “We have no intention of abandoning the monitoring of discharges. We feel strongly that operators should undertake a degree of self-monitoring to ensure that they are compliant with the requirements of their licence. We will require operators to report their monitoring information to Sepa."

He said the new strategy would apply to all those that Sepa regulated including those who are responsible for discharges to water, emissions to air and management of waste.

He said: “It is normal practice across the UK and Europe for regulators to require operators to undertake self-monitoring and to report the results. Clearly, the regulator has to put in checks and balances. We will be ensuring that our audit and environmental monitoring allows us to independently check the performance of sites. If operators cheat they will be misleading the public, damaging their reputation, and will possibly end up in court.”

Sepa later confirmed the strategy would also apply to nuclear sites, although an appropriate balance would be discussed in detail with the sector which was already involved in self-monitoring.

Highlands and Islands Green MSP John Finnie said: “Sepa’s role is a vital one, spelt out in their name, to protect our precious environment. While every citizen and business must play their part too, I am very concerned at Sepa’s plans to withdraw from monitoring discharges instead having businesses, regardless of their potential to have a negative impact on the environment, to ‘monitor’ themselves.

"I intend writing to the Cabinet Secretary about this change as I cannot imagine any meaningful risk assessment indicating these changes will enhance environmental protection or protect our vital water courses.”

A Scottish Water spokesman said performance-related payments were based on a number of agreed objectives being exceeded and are verified by external experts.