At least 24 people have died since the fires began in September. Air quality in the capital Canberra was this weekend rated the worst in the world.
Mr Morrison announced the creation of a recovery agency to help those who have lost homes and businesses in the fires.
He has faced fierce criticism over the speed of his response to the crisis.
The weekend saw some of the worst days of the crisis so far, with hundreds more properties destroyed. Rural towns and major cities saw red skies, falling ash and smoke that clogged the air.
Conditions eased in Victoria and New South Wales on Sunday after temperatures and wind speeds dropped and some light rain fell. But authorities warned that the danger was far from over.
"We're in uncharted territory," said the New South Wales premier, Gladys Berejiklian. "We can't pretend that this is something that we have experienced before. It's not."
John Steele, 73, who was evacuated with his wife from their rural property north of Eden late on Saturday, told the AFP news agency: "Visibility was down to about 50 metres, if that, and we had lots of debris falling out of the sky and a lot of white ash.
"The sky is still red. We're not out of the woods yet."
Prime Minister Morrison on Saturday announced the largest military call-up in the country's recent history, mobilising up to 3,000 reservists to assist exhausted volunteer firefighters.
Mr Morrison, who cancelled a planned visit to India because of the crisis, faced further condemnation on Sunday, after the head of the NSW Rural Fire Service revealed the service had only learned of the plan to call up reserve troops through the media.
In an indication of the long road ahead, Mr Morrison warned that the fires might burn for many months, and said that the newly-created recovery agency would run for at least two years. The body will help bushfire-hit communities recover, media reports said, through work ranging from rebuilding infrastructure to providing mental health support.
Queen Elizabeth on Sunday said she was "deeply saddened" by the fires, and thanked the emergency services "who put their own lives in danger" to help communities.