“It is an incredible kick in the teeth to the agents and prosecutors who toil away every day under very difficult circumstances to achieve justice and some restitution to the taxpayers from the billions of dollars that has literally been stolen from them,” Mr. Pelletier said.

His frustration is shared by many current and former Justice Department officials who spent years working on these cases, considered two of the most important taken up in the nationwide effort to combat widespread Medicare fraud.

“It is disheartening, demoralizing,” said Wifredo A. Ferrer, a former United States attorney for the Southern District of Florida, speaking generally about presidential commutations in Medicare fraud cases. “We are doing these cases to control health care costs and save lives and make sure legitimate health care centers don’t have to compete with the crooks.”