Wastewater companies like Southern Water have been given the green light to pump sewage that has not been fully treated into sensitive waterways.
The Environment Agency has told water firms they can temporarily reduce the amount of chemicals used, due to the national lorry driver shortage.
The Chichester Harbour Trust has now spoken out about the decision and said the harbour already receives a disproportionate amount of wastewater.
A spokesperson for the trust said in a statement today: "The Chichester Harbour Trust is concerned that the recent advice to water companies by government, removing the requirement to permit discharges if affected by supply-chain issues, gives the green light to operators to continue to pump untreated discharge into sensitive water bodies without recourse.
“The harbour already receives a disproportionate quantity of waste water through storm discharges, and the fundamental infrastructure provision needs to be improved significantly.
"We feel this acts as a nail in the coffin for the fragile ecosystem of Chichester Harbour, and undermines all our efforts and progress to secure greater protection for this unique environment."
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