Around 1.2 GB of data, amounting to at least 4,000 files, was stolen in the ransomware attack on Christmas Eve.
The environmental regulator confirmed that data stolen by what was likely to be international serious and organised cyber-crime groups has now been illegally published online.
The agency said priority regulatory, monitoring, flood forecasting and warning services were continuing to adapt and operate.
SEPA chief executive Terry A’Hearn said: “We’ve been clear that we won’t use public finance to pay serious and organised criminals intent on disrupting public services and extorting public funds.
“We have made our legal obligations and duty of care on the sensitive handling of data a high priority and, following Police Scotland advice, are confirming that data stolen has been illegally published online.
“We’re working quickly with multi-agency partners to recover and analyse data then, as identifications are confirmed, contact and support affected organisations and individuals.”
SEPA said the stolen data was primarily related to business dealings, including its work with international partners and corporate plans.
Personal information relating to a number of the agency’s staff is also thought to have been accessed during the hack.
The attack has left SEPA unable to access most of its systems, including its email system as well as its hourly rainfall and water level trackers.
The environmental regulator said it was continuing to respond to a “significant and sophisticated cyber-attack and a serious crime against SEPA” and was being supported by Scottish Government, Police Scotland and the National Cyber Security Centre.
It said it does not yet know, and may never know, the full detail of the 1.2 GB of information stolen, some of which will have been publicly available, whilst some will not have been.
Mr A’Hearn added: “Sadly we’re not the first and won’t be the last national organisation targeted by likely international crime groups.
“We’ve said that whilst for the time being we’ve lost access to most of our systems, including things as basic as our email system, what we haven’t lost is our 1,200 expert staff.
“Through their knowledge, skills and experience we’ve adapted and since day one continued to provide priority regulatory, monitoring, flood forecasting and warning services.
“Whilst some systems and services may be badly affected for some time, step-by-step we’re working to assess and consider how we recover.”
Police Scotland said that organisations and individuals should not seek to search for the stolen information, as accessing the host site may place organisations, individuals and their computer infrastructure at risk.
Detective Inspector Michael McCullagh of Police Scotland’s Cybercrime Investigations Unit said: “This remains an ongoing investigation.
“Police Scotland are working closely with SEPA and our partners at Scottish Government and the wider UK law enforcement community to investigate and provide support in response to this incident.
“Enquiries remain at an early stage and continue to progress including deployment of specialist cybercrime resources to support this response.
“It would be inappropriate to provide more specific detail of investigations at this time.”