The water firm said “there are no straightforward solutions and it had “reviewed its “proposals to include secondary wastewater treatment” after speaking with the local community.
SWW added: “This will require further technical assessments to address the significant challenges of operating on the islands, particularly the transportation and disposal of the resulting sludge.
“We are also progressing plans to upgrade Bishop and Wolf pumping station and install a new rising main to transfer wastewater to a new treatment plant.”
Partially treated wastewater is currently discharged from an outfall on a different part of the island.
Clarissa Newell from the EA said: “We recognise South West Water must improve wastewater infrastructure on the Isles of Scilly; a community where the economy relies on the quality of the environment and with logistical challenges for engineering works.
“Our position reflects government policy that any coastal discharges serving communities with over 2,000 people needs secondary treatment.”
The EA said the outfall and screen application would be reviewed but added the responsibility was on SWW to make the case for an alternative approach to secondary treatment.
The Isles of Scilly Wildlife Trust said the proposal to discharge sewage into a designated Marine Conservation Zone was “unacceptable”.
It said: “Should the regulators and industry judge that there are greater environmental costs of treatment and shipping sludge off Scilly than disposal of screened sewage at sea, then we wish to see the justification to this argument.”
A public consultation is set to take place within 30 working days of the permit application being made so people can give their views on the proposals.
Follow BBC Cornwall on X, external, Facebook, external and Instagram, external. Send your story ideas to spotlight@bbc.co.uk, external.
