The discovery is likely to revive criticism of the foreign trainee program, which has been accused of placing workers in substandard conditions and jobs that provide few opportunities for learning, the government said Friday.
The misconduct was uncovered in a probe by the Justice Ministry conducted after three Vietnamese trainees, who were in the country to learn professional skills, were found in March to have participated in cleanup work in Fukushima.
The Vietnamese were supposed to do work using construction machines according to plans submitted by the company.
"But they joined simple cleanup work such as removing soil without machines," an official told AFP.
A powerful earthquake in March 2011 spawned a huge tsunami that led to meltdowns at the Fukushima nuclear plant, causing the world's worst such accident since Chernobyl in 1986.
The justice ministry said after the discovery this March that decontamination work was not appropriate for foreign trainees.
One of the four companies has been slapped with a five-year ban on accepting new foreign trainees, and the ministry is still investigating how many trainees in the other three firms were involved.
The ministry has finished its investigation into 182 construction companies that hire foreign trainees, and will look into another 820 firms by the end of September.
Japan has been accepting foreign trainees under the government program since 1993 and there were just over 250,000 in the country in late 2017.
But critics say the trainees often face poor work conditions including excessive hours and harassment.
The number of foreign trainees who ran away from their employers jumped from 2,005 in 2012 to 7,089 in 2017, according to the ministry survey. Many cited low pay as the main reason for running away.
The investigation comes as Japan's government moves to bring more foreign workers into the country to tackle a labor shortage caused by the country's aging, shrinking population.
The government in June said it wanted to create a new visa status to bring in foreign workers, with priority given to those looking for jobs in sectors such as agriculture that have been hardest hit by the labor shortage.
The workers would be able to stay for up to five years, but would not be allowed to bring their family members.
The government put the number of foreign workers in Japan in 2017 at 1.28 million people.
But more than 450,000 of those are foreign spouses of Japanese citizens, ethnic Koreans long settled in Japan, or foreigners of Japanese descent, rather than workers coming to Japan simply for jobs.
Another nearly 300,000 are students.