The refugee accommodation at the MalmöMässan hall, which has already been criticized by several Swedish charities, was singled out in the agency's weekly report assessing the refugee situation in Sweden.
“Save the Children says that certain arrival accommodations and other temporary accommodation places where children are present is highly inadequate. These include MalmöMässan which does not meet international standards for refugee camps in the availability of toilets, showers and health care,” said a summary of the document on the agency's website.
“Children with special needs may not be given the support they are entitled too,” it continued.
The Swedish Civil Contingencies Agency (MSB) is responsible for issues linked to public safety and civil defence in the Nordic nation.
Despite a dip in the number of refugees arriving in Sweden following recent tighter border checks and a government announcement that it would cut the number of residency permits made available, MSB's report suggests that Malmö, a key entry point to the Nordic nation, is still struggling to cope.
The agency added that there had been a number of reported disturbances at accommodation for asylum seekers around the country, noting that this was likely prompted by “overcrowding, uncertainty about the future and mental illness” among temporary residents.
Ulf Sempert, head of the Skåne region's police operation handling the refugee crisis, told Swedish tabloid Aftonbladet on Thursday that he understood that fighting was also linked to ethnicity.
“There are people who come from war-affected areas and people of different ethnicities and they do not have the same understanding of things,” he said.
Sweden's Migration Agency announced earlier this week that it was planning to hire more security guards at major refugee venues.
MSB's report follows recent media interviews with a number of refugees staying at MalmöMässan, one of the venues used when Sweden hosted Eurovision Song Contest in 2013, who described the conditions inside the conference hall as “inhuman” and “like a prison”.
A policeman from Stockholm sent to help keep order wrote on Facebook that he had had trouble breathing inside the centre, because it was so crammed full of people.
Officials from Sweden's Migration Agency explained last week that refugees only spent an average of 16 hours in the hall before being moved on and said that staff were working to improve sanitation.