Police now suspect that many of the arrested workers could have been victims of human trafficking.
"That was not in our minds when we started, but after interviews we are having a closer look," said Stefan Hagberg at the Swedish border police told the Aftonbladet daily.
Police officers raided the factory just as many were arriving for work at 8am on Thursday.
According to Aftonbladet the majority of those arrested in the raid come from Uzbekistan or other former Soviet republics.
When the police arrived at the factory in Jordbro south of Stockholm there were 54 people working in the factory, 32 were detained and taken from the premises.
Eat Food Factory's owner Murat Korkmaz played down the significance of the raid.
"There is nothing untoward. The police often carry out these kinds of checks. They are just checking that the identity papers in the the employees' paper checks out," he said to Aftonbladet.
Korkmaz told the newspaper he felt let down by his employees, claiming they tricked him with false papers.
The raid isn't the first time the company has been hit with suspicions of sub-standard labour practices.
In 2008, when the company was called Mo Catering, workers described how asylum seekers and undocumented workers were forced to work under “slave-like” conditions.
However, the accusations were denied by company officials, who claimed the complaints were unfounded.