Apple will pay $25 million in backpay and civil penalties to settle allegations that it favored visa holders and discriminated against US citizens and permanent residents during its hiring process, the Department of Justice said in a statement on Thursday. This is the largest amount that the DOJ has collected under the anti-discrimination provision of the Immigration and Nationality Act.

At the heart of the issue is a federal program administered by the Department of Labor and the Department of Homeland Security called the Permanent Labor Certification Program (PERM). PERM allows US employers to file for foreign workers on visas to become permanent US residents. As part of the PERM process, employers are required to prominently advertise open positions so that anyone can apply to them regardless of citizenship status.

The DOJ said that Apple violated these rules by not advertising PERM positions on their recruiting website, and also made it harder for people to apply by requiring mailed-in paper applications, something that it did not do for regular, non-PERM positions. As a result, a DOJ investigation found that Apple received few or no applications for these positions from US citizens or permanent residents who do not require work visas.

As part of the settlement, Apple will pay $6.75 million in civil penalties and set up a $18.25 million fund to pay back eligible discrimination victims, the DOJ’s statement said.

Apple disagreed with the DOJ’s characterization. “Apple proudly employs more than 90,000 people in the United States and continues to invest nationwide, creating millions of jobs,” a company spokesperson told CNBC. “When we realized we had unintentionally not been following the DOJ standard, we agreed to a settlement addressing their concerns. We have implemented a robust remediation plan to comply with the requirements of various government agencies as we continue to hire American workers and grow in the US”