The paleontology collection held several key specimens of pterosaurs, Kellner's specialty, dinosaurs, and other prehistoric animals of South America.
It's the country's equivalent of having The Smithsonian National Museum of Natural History in Washington DC, or the Natural History Museum in London, turn into nothing more than cinders in a matter of hours.
"For us [Brazilian people], Luzia is the ultimate Brazilian", Ana Cristina, a 45-year-old who works for the Municipality of Rio de Janeiro state, told ABC News.
"What happened isn't just regrettable, it's devastating, and politicians are responsible for it.""My feeling is of total dismay and enormous anger".
Video broadcast on Brazilian TV showed that the fire had spread throughout all parts of the building.
Sa Leitao, who in July 2017 became culture minister under Temer - a deeply unpopular center-right leader - acknowledged that "the tragedy could have been avoided" but said "the problems of the National Museum have been piling up over time".
And although the cause of the fire has not yet been identified, Ms McKay said the event was an important reminder that museums receive the necessary funding to mitigate risks such as fire.
"Very little will be left", preservation director Joao Carlos Nara told Agencia Brasil.
"History cannot be measured by the damage to the buildings that housed the royal family during the Empire".
The collection also contained a painting by the Brazilian artist Candido Portinari and extensive paleontological, anthropological and biological specimens.
Latin America's largest nation has struggled to emerge from its worst recession in decades.
Riot police fired tear gas outside the park housing the museum on Monday as a small, irate crowd tried to enter.
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"We Brazilians only have 500 years of history".
"They're burning our history, and they're burning our dreams". The Folha de S. Paulo newspaper reported in May, as the museum was preparing to celebrate its bicentennial, that its annual budget had fallen from around $130,000 in 2013 to around $84,000 previous year. This year was on track to include an increase from last year.
One of the museum's prized possessions was "Luzia" - the skull and bones of a 25-year-old woman dating back 11,000 years ago.
Kellner said the institution had recently secured approval for money for a planned renovation, including an upgrade of the fire-prevention system.
"Look at the irony".
The National Museum's press service told local reporters that four security staffers had been evacuated in time.
There were no reports of injuries, the museum said, and it wasn't immediately clear how the fire began. Instead, trucks had to gather water from a nearby lake.
The museum's current director, João Carlos Nara, said the damage was "irreparable". "Two centuries of science and culture are lost forever", said Sergio Alex Azevedo, a paleozoologist and former director at the museum.
Between 2013 and 2017, the National Museum in Rio's federal funding fell about a third, to 643,567 reais, according to official budget data.