About 300 staff are facing redundancies, with local authorities having no idea how they will cope with reduced guards.
According to Sweden's Migration Board the cuts will focus mainly on the central region.
Migration manager Magnus Önnestig said in a statement: "All counties and localities in the region affected by the layoffs.
"The reduction will primarily be achieved through redeployment and natural attrition, but redundancies can not be ruled out.
The issue of immigration in Sweden has sparked anger on the streets
All counties and localities in the region affected by the layoffs
"Exactly how various localities and units within counties will be affected remains to be seen.
"Local groups are now working to plan the transition and developing proposals for an organisational structure.
"To conduct negotiations with employee organisations locally and regionally.
The Neo Nazi movement is on the rise in Sweden
"The goal is to find the best solutions possible for the employees affected."
Sweden had a record number of asylum seekers in 2015 with 163,000 applications.
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However those who travelled to the country were frustrated due to a lack of work.
Sweden erected a fence at its border with Denmark
The Government then introduced a scheme to offer individual asylum seekers £3,500 or £8,500 to families if they withdrew their applications and left.
That policy is said to be partially responsible for a record 4,542 asylum seekers invalidating their applications in the first eight months of 2016.
However another key reason is said to be a lack of work for migrants and long processing times as the Government puts the bill of accommodate asylum seekers to £4.8 billion in 2016.
Sweden has built refugee camps to accommodate those who fled there
Sweden has seen unprecedented unrest over the past few years with protests for and against the country's migration policy.
Last week the European Commission said the passport-free Schengen zone country should be allowed to extend its external border control measures for an additional three months.
Of the almost 163,000 people who arrived in the country fleeing their homes, less than 500 found a job.
Last year, Ylva Johansson, the Minister for Employment and Integration said: “Most Swedes are not racist.
“But when there is this special asylum housing when they cannot work, and cannot be part of society this is really a tension.
The UK Reacts To Trump's 'Muslim' Travel Ban
Mon, January 30, 2017
President Trump signed an executive order banning immigration to the USA from seven 'muslim' countries. This led to protests across America and, now, the UK.
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People demonstrate during a protest at Downing Street in central London against US President Donald Trump's controversial travel ban on refugees and people from seven mainly-Muslim countries
"This is a dangerous situation; we have a lot of people in no-man's land … living outside society.”
The news comes as Sweden’s Migration Agency announced it accepted 77 percent of the 112,000 asylum claims it processed in 2016.