Since a devastating fire gutted Rio’s National Museum and consumed most of its collection of 20m items, archaeologist Murilo Bastos, 35, has lived an upside-down life.

He used to work in an office inside the colonial palace, once the home of the Portuguese royal family. Now he scours its charred interior for anything that survived the blaze.

“We were used to working in air conditioning, now we are on a building site,” he said, stamping dusty boots as he took a break outside its sealed-off perimeter on a recent morning. The museum’s outer walls are still standing but three of its interior floors collapsed.

“We don’t work in the field. The field came here,” he said.

The fire in September was an unthinkable tragedy for academics like Bastos, many of whom started out at the museum as interns and watched helplessly as irreplaceable archives went up in smoke. Yet some have found new meaning in the rescue work, celebrating each of the 1,500 finds made so far – including indigenous bowls, arrowheads and an axe – no matter how blackened or broken. They hope a new National Museum can emerge from its ashes.

People watch as flames engulf the 200-year-old National Museum of Brazil in Rio de Janeiro on 2 September 2018. Photograph: Leo Correa/AP

“The museum is alive,” Bastos said. “The rescue is paying off. We are recovering things.”

A key moment was the rediscovery of “Luzia” – the 11,500-year old skull of “the first Brazilian woman” believed lost in the fire, then rescued in fragments from the remains of a metal cupboard. “It was a symbolic moment,” said historian Regina Dantas, 56.

Six days a week, the 60-strong recovery team picks through the ruins; their findings are taken to a screening area, examined by specialists and stored in containers.

Archaeologist Claudia Rodrigues-Carvalho, the team’s coordinator – and the museum’s former director – said that by February the building should be secure enough for proper excavation work to begin.

“I never never wanted to be here, doing this, but as it happened I can’t imagine being anywhere else,” she said.

For decades, museum directors had pleaded for more money to protect the wooden-floored museum, she said. In June, as the museum celebrated its 200th birthday, Brazil’s government development bank finally agreed to $5.6m for restoration work. But none of it had arrived when the fire broke out.

“I felt defeated. I worked intensely to prevent this,” she said. “[But] the museum did not have a budget.”

In 2017, the museum’s budget was just $203,000 to care for Brazil’s most precious collection of historical, biological and anthropological items. Two years earlier, Rio spent $54m on a shiny Museum of Tomorrow – whose exhibitions are digital.

The museum’s anthropology, ethnography, palaeontology, geology, entomology, arachnology and malacology collections were all housed in the palace – and most of them were destroyed, she said. The botany, invertebrate and vertebrate collections were kept in separate annexes and survived.

The losses are thought to include indigenous feathers, textiles and insects kept in glass cases, though some fibres may have survived from the museum’s mummies and indigenous textile collections. Rock, metal and porcelain items were more likely to have resisted the intense heat, she said.

Police are still investigating the causes of the blaze, but the museum’s current director, Alexander Kellner, said he was well aware of the fire risk when he took office in February, but was unable to install a safety system in time.

A researcher holds an original amethyst, left, and an amethyst which was transformed into a yellow citrine stone due to the high temperatures caused by the fire that swept through the National Museum in September. Photograph: Léo Corrêa/AP

“We knew we didn’t have the necessary protection,” he said, “fire doors, sprinklers, things like that. But in a listed building, with a very diverse archive, you can’t do whatever you want.”

Museum staff have not been given a reopening date but a spokeswoman said it would take three years. Whenever it does reopen, a top priority for Kellner will be to reach more Brazilians.

Fewer than than 200,000 people visited in 2017; in its first eight months, the Museum of Tomorrow attracted a million visitors. “A museum that doesn’t talk to society is condemned to extinction,” Keller said.

Nycoly Tavares, 21, a biology student at Rio’s Federal University studying fish at the museum, said the aloofness of academics kept them distant from working-class Brazilians like herself.

“The teachers were like gods, they stayed in their rooms. They have to change this,” she said. “We have to keep the museum growing.”

New interactions between society and the museum have already begun.

A commemorative stamp was issued in December at a ceremony where musicians performed a song in honour of its Bendegó meteorite – which also survived.

A Rio tattooist has been inking free museum tattoos on the arms of staff and students, a project organised by palaeontologist Beatriz Hörmanseder, 26, a graduate student who studied prehistoric crocodiles from the museum’s collection. “The tattoos helped me,” she said. “I lost all my work.”

Archaeologist Angela Rabelo shows artefacts rescued from the ashes of the fire that swept through Rio’s National Museum in September. Photograph: Léo Corrêa/AP

For her master’s degree at Rio’s Federal University, she was studying a 110m-year-old Brazilian crocodile, found in a lake bed in the north-east. It had never been studied. “It could have been a new species,” she said. But she had not yet scanned the fossil, whose skeleton was remarkably complete.

And now all that is left of it are some photographs, her notes, and its catalogue number, tattooed under the museum’s image on her left forearm.

Classes continue at the museum in a separate complex. And Hörmanseder has found a new crocodile fossil to study – 35m years old and from Utah – which was in a government deposit. It’s not the same. But it’s better than nothing.

“I really liked the Brazilian one,” she said. “I want to keep working and help rebuild the museum, in any way we can.”