The federal government is cracking down on the U.S. organ transplant system, investigating donation groups accused of safety lapses and overhauling policies meant to protect donors and recipients.

The efforts come after congressional scrutiny and reporting in The New York Times revealed troubling problems in the system, including at organ procurement organizations, the nonprofit groups in each state that arrange transplants. A federal investigation recently found that the organization in Kentucky had ignored signs of growing alertness in critically ill patients being prepared for organ donation.

The U.S. Department of Health and Human Services has begun investigating other nonprofits over similar accusations, as well as reining in others that flout fairness rules by sending organs to patients who are not near the top of waiting lists.

The initiatives were described in an interview with Dr. Raymond Lynch, the transplant chief at the Health Resources and Services Administration, an agency within H.H.S. that oversees the system. “We want to make sure that people continue to have faith in the public good that is organ procurement and transplant,” he said. “We will make it safe and reliable.”

Dr. Lynch declined to name the targets of the investigations but said the inquiries were focused on circulatory death donation, an increasingly common practice.

Unlike most donors, who are brain-dead, these patients have brain function. But they are on life support, often in a coma, and are not expected to recover. If donation is authorized, doctors withdraw life support, wait for the patient’s heart to stop and then remove the organs. This type of donation involves judgment calls that can be prone to error.