Guatemala is observing three days of mourning over the tragedy. President Jimmy Morales has fired the director of the shelter, which was badly overcrowded and the target of multiple accusations of sexual and other abuse by staff.
The latest toll updated a previous count of 29 dead. All the victims were aged between 14 and 17.
An investigation is underway into the cause of the blaze, which happened early Wednesday in the female living section of the Virgin of the Assumption Safe Home located just to the east of Guatemala City.
"How is it they didn't realize in time to save them if the smoke was seen right away?" asked the uncle of one deceased 15-year-old at the capital's morgue. The man gave only his first name, Marvin. The charred remains of his niece were identified through a DNA sample.
Initial media reports suggested the fire was started by some of the young residents in the shelter during a rebellion against conditions inside. A small group of them had reportedly escaped late Tuesday, before the disturbance.
Officials said 19 girls died at the scene, and dozens were injured, many critically. Some of those patients succumbed to their burns overnight and early Thursday.
Badly overcrowded
"They were serving food to the teenagers when some of them started a fire in a mattress and that's how the fire was set," said Abner Paredes, a prosecutor defending children's rights.
The shelter was designed to house around 400 children but was holding nearly double that at the time of the fire.
It is run by the government, under the supervision of the social welfare ministry. The residents included children escaping domestic violence, abandonment, street living, and former juvenile delinquents.
President Morales said that before the fire, orders had been given to transfer some of the youths to other facilities because of the overcrowding.
A group of activists deposited burned mattresses in front of Morales' presidential palace on Thursday to denounce alleged negligence by the authorities.
A 'time bomb'
"It was a ticking time bomb. This was to be expected," one of the center's former employees, Angel Cardenas, said outside the facility on Wednesday.
He said he had lodged several warnings about conditions inside.
Rosa Aguirre, a 22-year-old street vendor who rushed from the capital to see if her two sisters, aged 13 and 15, and her 17-year-old brother were among the casualties, said authorities had given no information to relatives.
She said she, too, had lodged complaints about how the center's residents were treated, but received no attention.
She said brawls often broke out inside, and her brother was sometimes put in a dark isolation cell nicknamed the "chicken coop."
She said she had tried in vain to gain custody of her siblings after their mother's death four months ago.
The shelter has been the target of multiple complaints alleging abuse. Dozens of children have run away in the past year, reportedly to escape ill treatment.
Calls to close shelter
A prosecutor for upholding children's rights, Hilda Morales, told reporters she was seeking to have the shelter closed due to authorities' inability to manage it and the series of complaints.
She noted that last year the Inter-American Commission on Human Rights had found in favor of several adolescents who had alleged mistreatment and sexual abuse in the shelter.
Another prosecutor tasked with protecting children in the country, Harold Flores, told the radio station Emisoras Unidas that since last year, complaints had surged from minors who fled the shelter alleging sexual abuse.
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