SAN FRANCISCO—San Francisco city officials have ordered that the San Francisco Roman Catholic Archdiocese to pay $3 million in health care costs to its workers after city officials found the archdiocese violated a local health care ordinance for more than 1,000 of its workers.

The archdiocese also faces $113,000 in penalties from the city of San Francisco.

“It’s important for us to ensure that workers are made whole,” said Pat Mulligan, director of San Francisco’s Office of Labor Standards Enforcement to the SF Chronicle.

The SF Roman Catholic Archdiocese violated the Health Care Security Act law, which requires businesses with more than 20 San Francisco employees who work more than eight hours a week to pay into a health care plan or a savings account for those employees.

A city audit of the archdiocese records show that from October 2009 to June 2016, they did not pay into those required funds for the majority of its 1,722 employees who are covered by the law.

“While we don’t concede we are in violation, we also don’t believe that the numbers are correct, and we are working in good faith with the city to find the right figures,” said Mike Brown, a spokesman for the archdiocese told the SF Chronicle.

Most of the archdiocese’s employee’s work at Catholic schools and churches and none of the disputes have involved the city.