The National Board of Forensic Medicine told reporters it would begin age tests in early 2017.
Forensic examiners will determine whether an asylum seeker is over or under the age of 18 based on dental assessments of wisdom teeth and magnetic imaging of the knee joint.
"There's no method to medically determine the exact age of an individual... But by studying which phase a person is in, you can draw approximate conclusions," forensic examiner Elias Palm said.
The tests will be voluntary, meaning that an individual can refuse to undergo them.
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A spokesman for the Migration Agency, Fredrik Bengtsson, told AFP that minors wanting to prove their real age would welcome the tests.
Those who refuse run the risk of having case handlers determine that they are adults.
Sweden has taken in more unaccompanied child asylum seekers than any other country in Europe.
In 2015, the Scandinavian country took in more than 35,000 unaccompanied children, 90 percent of whom were boys and many of whom do not have identification papers.
According to the Migration Agency, there are age doubts in 70 per cent of cases where asylum seekers claim to be between the ages of 15 and 17.
Swedish officials have also expressed concern that some adults passing themselves off as children are being placed in housing centres for children, putting the younger children at risk.
In one case that garnered nationwide, attention, a 12-year-old boy from Afghanistan was raped by two other self-proclaimed "boys" living in the same housing centre for children.
The National Board of Forensic Medicine, which will outsource the testing, said that there would likely be between 4,000 and 18,000 tests carried out overall.