The crimes go back at least to 2009, prosecutors said.
Also charged is Alberto Diaz-Hernandez, a 33-year-old Century Roofing employee who is a citizen of Mexico. He's charged with one count of transporting, harboring or encouraging people who are unlawfully in the country to stay.
All three men entered not-guilty pleas at a hearing Tuesday afternoon in federal court in Kansas City. Their attorneys all declined to comment to The Associated Press.
Century Roofing, which says on its website that it has been in business since 1990, mainly used workers who are in the country illegally to complete commercial and residential roofing projects in the Kansas City area, the indictment says.
Roofing crew leaders were paid in cash and threatened with being fired if they didn't pay kickbacks to the company owners, prosecutors said.
The owners also threatened to call federal immigration agents if crew leaders or their crews failed to pay kickbacks, worked for other roofing companies without permission, or missed deadlines for finishing a job, prosecutors said.
"Unlawful business practices alleged in the indictment paint a picture of undocumented workers being manipulated by employers who played on their vulnerabilities particularly their fear of being caught and deported from the United States," Acting U.S. Attorney Tom Beall said.
The indictment includes a criminal forfeiture count seeking real estate, proceeds from bank accounts and substitute assets, if necessary.
The labor trafficking and conspiracy counts each carries a maximum sentence of 20 years in prison and $250,000 fine, while the transporting and harboring count has a maximum five-year sentence and $250,000 fine.