The number of young girls who died in a fire at a children's shelter in Guatemala shot up to 39 even as many of the victims continue to be in a serious condition.

Officials at Roosevelt Hospital in Guatemala City said two girls succumbed to their injuries on Saturday (11 March) in the fire that started when mattresses were set on fire while residents protested at the government-run shelter for children with disabilities, abuse victims and young offenders.

Carlos Rodas, the head of child protective services agency, was ordered by a judge not to leave the country as investigations into the case continue, according to the Associated Press.

President Jimmy Morales blamed the government's "insensitive" and "rigid" system for the way it treats troubled young people and vowed to reform protection services. He also charged that all government institutions in charge of youth shelters had a role in the tragedy.

Carlos Soto, administrator of the San Juan de Dios hospital that treated many of the burn victims said medical specialists had arrived from Texas to evaluate the victims' condition.

Soto said at least four of them could travel to the US for treatment and added that the adolescents had burns on their faces, legs and torsos.

The incident has sparked a huge controversy in the country as questions remain as to why some at the shelter set mattresses on fire and if the doors were locked as the girls pleaded for their life.

Thousands of Guatemalans protested in the capital city against the government as they read out the names and ages of the victims.

Guatemala children's shelter
Candles forming the number 34 during a protest outside the presidential house in Guatemala CityJohan Ordonez/AFP