"Multiple" employees at facilities operated by Southwest Key participated in the abuse, the Justice Department stated in a press release.
The "severe or pervasive" abuse included "sexual contact and inappropriate touching, solicitation of sex acts, solicitation of nude photos, entreaties for inappropriate relationships, and sexual comments," the statement claimed, according to RT.
The sex crimes allegedly occurred between 2015 and 2023, while Southwest Key received billions of dollars in government contracts to house unaccompanied minors caught crossing the US-Mexico border illegally.
The company, which operates 29 shelters in Texas, Arizona, and California, "took insufficient action to prevent sexual harassment of the children in its care," the statement continued.
In some cases, children were discouraged from reporting sexual harassment and threatened if they spoke up about the abuse.
The lawsuit, filed in Texas, is separate from multiple criminal complaints filed against Southwest Key employees since 2017.
It accuses the company of violating the Fair Housing Act by allowing the abuse to take place, seeking an undisclosed financial sum from the company, and a court order requiring the firm to "take appropriate steps to prevent such harassment in the future."
Southwest Key describes itself as "one of the largest, Latino-led nonprofit organizations in the United States," with its website stating that its staff work "on the frontline of social justice, youth advocacy, and immigration."
Southwest Key was founded in the late 1980s, and during the years covered in the lawsuit, received funds from the administrations of Barack Obama, Donald Trump, and Joe Biden.
It is unclear how many children are currently housed in Southwest Key facilities, although the company has space for more than 6,300 kids at its network of shelters.
Illegal border crossings of both children and adults have soared under President Biden's administration, with Customs and Border Protection agents encountering nearly 8.2 million migrants at the southern border since Biden took office in January 2021, compared to 5.5 million during Obama's two terms and Trump's single term combined.