The two boys, both of whom are younger than ten, were circumcised on Sunday.
"The police received a call on Sunday from someone who had heard the boys screaming," local police spokesman Göran Gunnarsson told the TT news agency.
The police encountered a 36-year-old woman, believed to be related to the boys, at the scene. She has been arrested on suspicion of aggravated assault, as it is illegal to perform a circumcision without the procedure being supervised by a medical professional.
In 2001, the Swedish parliament passed a law to protect boys against being circumcised without a professional present. The legislation was designed to safeguard them against discomfort, pain, as well as help prevent potential infection.
The prosecutor assigned to the case in Eksjö told Sveriges Radio (SR) that the boys were doing well despite the circumstances.
The bulk of male circumcisions in Sweden take place withing the Jewish and Muslim populations, with the practice being extremely rare in the wider population. According to a September 2012 report by Sveriges Television (SVT), Swedish health authorities estimate that around 3,000 male circumcisions take place in the country each year.
"You've got to be practical. We can't say 'You can't circumcise your children because we don't do that here in Sweden', because it will happen anyway," Gothenburg paediatrician Tomas Arvidsson told SR in 2006.
"Which means we have to perform circumcision, and the least we can do is to have certified personnel to take care of the operation."
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