Zoo staff are working to account for all species after fire destroyed much of the vast plastic roof covering Chester Zoo's Monsoon Forest area.
All the mammals have been located but keepers are "working hard" to track down the rest of the animals, according to a statement released by the zoo on Saturday.
However attempting to trace all the animals, which includes birds, will take "some time", they add.
Eyewitnesses described how visitors to the attraction - billed as the largest indoor zoo exhibit in the UK - were rushed to safety as the blaze spread rapidly through the polymer roofing material.
Zoo staff led the animals housed in the structure to safety as firefighters rushed to the scene.
Orangutans, gibbons, crocodiles, turtles and exotic birds are among the species housed in the Monsoon Forest, which recreates a tropical south east Asian environment.
The fire was declared a major incident by Cheshire Fire and Rescue Service.
The zoo said in a statement: "Critically endangered Sumatran orangutans and other mammals are accounted for and being looked after by the zoo's specialist conservationists and vets.
"We are working hard to account for all other species, such as birds, and move animals to alternative habitats.
"Given that this is the UK's largest zoological tropical house, it will take some time.
"We will be working intensively in the coming days and weeks to do this."One person was treated for smoke inhalation as a result of the fire, according to North West Ambulance Service.
One eyewitness, David Clough, 50, who lives across the road from the zoo, said high winds fanned the flames in the roof of the building.
He added: "We were very worried for the people and animals that would have been in the building."
He added: "Orangutans and gibbons are our nearest neighbours there, but there are many other animals, including free-flying birds.
"It was spreading across the roof in strong winds for a while."
The zoo's statement added: "Visitors were evacuated and the zoo's response team worked alongside the emergency services to help bring the situation under control."
Cheshire Fire and Rescue Service crews wearing breathing apparatus tackled the blaze using water jets.
A visitor, who declined to be named, told the Press Association: "We were in the monsoon enclosure when it happened and were rushed out due to an electrical fire. It spread very quickly.
"The staff ensured all the members of the public were safe. Many staff (were) running towards the fire, (I'm) assuming to help with evacuating animals.
"The entire zoo is closed - a shame as we've travelled up from Plymouth."Although the fire has been extinguished firefighters will remain at the scene to dampen it down, a statement from the fire service said.