The Western Trust said on Saturday patients would be returning to wards and the hospital is progressing to "normal activity" after patients from seven wards were evacuated in the major incident.
A&E consultant Alan McKinney said he hoped by the end of Saturday that patients up as far as ward six would return and ward seven by the end of the weekend.
"By Monday, Tuesday, we should be fully back to normal again," he said.
Northern Ireland Fire and Rescue service are currently investigating the cause of the fire, but it is understood it began on the roof of the 11 storey building which was reported at around 6.20pm.
Barry McDowell from NIFRS said because the fire was on the very top of the building it was very difficult to deal with-around 50 firefighters and 11 fire engines attended the scene.
He said a pipe had also burst during the blaze and has caused damage throughout the premises.
"The scale of that evacuation was huge for us," he said.
The hospital's Emergency Department remained opened to patients throughout the incident and continues to operate as normal, however operations had been postponed.
The Trust has asked that visiting is kept to a minimum and said that staff will make contact with family members with regards to the location of their relatives who have been relocated elsewhere within hospital.
We have known that we've been carrying a fire risk because of the age of the building, because of the electrics in that building and it is due for refurbishment.
Gerard Guckian, Western Trust
There was a known "fire risk" at the hospital according to the Western Trust chairman Gerard Guckian.
He said: "We would like to assure the public that first off, no patient has been harmed in this incident."
He said the fire had broken out in an older part of the building.
"This is the oldest part of the hospital, and this a hospital that was the first hospital built after the Second World War," Mr Guckian said.
He added: "If you just look at the hospital you can see the new part of the hospital already built, unfortunately the older parts then carry that risk but we have taken steps to mitigate that risk and we wouldn't like to say at this stage what has caused the fire."
He said the risk had up until now been fully managed and added that "every building of any age carries a risk with it".
"Obviously we wish to have a new, state-of-the-art building but it takes some time for that to be constructed and bear in mind, unlike any other business, you can't shut down a hospital to rebuild it, we have to keep operating."
It is imperative that the Health Minister, hospital senior management, the Trust and the Health and Safety Executive immediately launch an inspection of the building and rapidly draw up an action plan to assure the public that they will be safe in the hospital wards.
Pat Ramsey, SDLP MLA
The majority of patients have been accommodated onsite and a small number of patients have been moved to other "appropriate health and care settings" in Londonderry.
Patients were evacuated from their wards earlier this month in a separate incident when a fire broke out on the seventh floor and hospital management have previously submitted proposals to the department of Health to make the building safer.
SDLP assembly member Pat Ramsey commended those involved in the evacuation but expressed concern that possible health and safety concerns around the Altnagelvin Hospital tower block were not acted on and has called for an immediate inspection.
The Foyle MLA said: "We had a serious situation which affected the lives of dozens of patients who expect their safety to be of paramount importance while they are being treated.
"We cannot play fast and loose with the lives of people already suffering illness or injury."
Health Minister Edwin Poots said:"In this instance the fire happened, we need to identify how it happened and ensure that such a thing doesn't happen again."
It's a demonstration that you do have these risks and therefore you have to seek to avoid those risks actually turning into a tragedy.
Health Minister Edwin Poots
He joined in praise for all the staff and volunteers who helped during the incident.
"These public servants give us all a reason to be proud," he said.
The Northern Ireland Ambulance Service said it was "proud of the efforts of all staff".
A total of, approximately 70 NIAS staff were involved in the operation, some who volunteered despite not being on duty.
"While it is fortunate that patients were not injured, this incident has demonstrated that the Major Incident plans of NIAS and other agencies involved are geared to ensure that challenges such as this are met and that the confidence in our emergency and support services is not misplaced," a statement said.
Regional Development Minister, Danny Kennedy paid tribute to Translink staff who provided assistance to evacuate patients.
Up to 13 buses and three managers went to the site as a back-up and support to the ambulance service staff who evacuated hundreds of patients from the hospital.
The Western Trust is operating dedicated helpline numbers on 028 7129 6202 and 028 7129 6204 for anyone concerned.