The government agency had previously predicted that 12,000 children and young adults would arrive in Sweden without a parent or other older relative.
But it has now revealed a new estimate of 30,000 to Swedish tabloid Expressen and public broadcaster SVT.
The announcement comes as Sweden struggles to find accommodation for record numbers of refugee arrivals of all ages.
Migrationsverket recently sent out a nationwide appeal for local councils and businesses to provide shelter as winter sets in.
But while theatres, sports centres and even a ski resort have opened their doors to refugees, the situation is much more complicated when it comes to unaccompanied children, as Swedish authorities seek to find them both foster care and schooling.
“More and more [local authorities] say they will be hard pressed to do it,” Per-Arne Andersson, head of department at the Swedish Association of Local Authorities and Regions (SKL) was quoted as saying by the TT news agency on Wednesday.
He said that only around 40 percent of children arriving in Sweden were able to be placed with friends or acquaintances, explaining that the rest of the arrivals of unaccompanied minors were distributed around the country, with some municipalities taking in a greater share than others.
“The situation does not look like is set to change, rather to continue,” he added.
Skåne in southern Sweden is among the regions struggling most with an influx of children and young adults and authorities have recently reported difficulties keeping track of the refugees.
Last week officials in Trelleborg told The Local that around 1,900 children had arrived in the town without guardians in the preceding month, but that at least half were believed to have since left the area without alerting officials, despite being given temporary accommodation there.
In 2014, 7,049 children travelled solo to Sweden and sought asylum, an increase of more than 80 percent on 2013.
A total of 95,430 people have launched asylum cases so far in 2015, Migrationsverket said on Monday.
Earlier this month Sweden surpassed a previous record set in 1992 of 84,016 people seeking sanctuary in the Nordic nation following fighting in the Balkans.