A new federal investigation of healthcare industry pay practices is underway after it came to light that many hospitals and nursing homes have not been paying proper overtime to their employees.

For example, hospitals and clinics operated by SSM Health Care, a Roman Catholic entity in St. Louis, recently paid more than $1.7 million in overtime back wages for 4,000 employees.

Boston’s Partners HealthCare System settled a charge by that they had violated the Fair Labor Standards Act by agreeing to pay 700 employees more than $2.7 million.

And in a class-action lawsuit settlement in California, Kaiser Permanente will pay $7.25 million to hundreds of employees who claim they were improperly classified as exempt.

The Labor Department has increased its staff by one-third, adding 250 new investigators devoted to uncovering employee underpayment.

The abuse appears to be widespread. Investigators in the Albany, New York, office reported that fewer than 36 percent of healthcare employers were in compliance with the federal wage-and-hour law. In Connecticut and Rhode Island, the department is focusing on residential healthcare facilities, while in Alabama and Mississippi, assisted-living and group homes are being targeted.

Many of the complaints related to work performed during lunch and other breaks. Federal regulations clearly state that hourly employees “must be completely relieved from duty” during bona fide meal periods. If work is performed, the employer must pay for it.

Several of the healthcare facilities who have been targeted by department investigators or class-action lawsuits are vigorously defending themselves. A spokesman for Kaleida Health, a large New York employer, characterized the suit files against his group as “frivolous.”