The trust reported ‘significant issues' with IT systems yesterday which led to the cancellation of most planned surgeries and out-patient hospital appointments.
Community services were expected to return to normal service today.
An ambulance divert has been stood down at Daisy Hill Hospital, however, a divert at Craigavon Area Hospital remained in place last night.
A trust spokesperson said: ‘It will take some time for normal business to be fully restored and we sincerely apologise once again for the disruption.
‘We ask that people avoid coming to our Emergency Departments unless absolutely necessary as we continue to prioritise critical care at this time.
‘The cause of the outage is still being investigated, however, there is nothing to indicate any cyber related issues.'
Health minister Mike Nesbitt said: ‘I want to pay tribute to clinical colleagues within the Southern Trust who continue to provide such compassionate and safe care to patients during these challenging circumstances.
‘While the specific cause of the outage is still being investigated, I would like to provide reassurance about the resilience of encompass. Even during connection issues, an individual's health record remains secure, and continuity of care is protected.'
