“You’re talking about issues that may drag out longer than a year,” Dr. Stimler said.

Most cases stop at the administrative law judge level; however, the timeline to get there has grown dramatically. In a memo released earlier this year, Nancy Griswold, the chief judge of the Office of Medicare Hearings and Appeals, suspended scheduling new hearings. She wrote, “We do not expect general assignments to resume for at least 24 months.” In a related hearing before Congress, Ms. Griswold presented data showing that that received appeals more than doubled, from 117,371 in fiscal year 2012 to 350,629 in fiscal year 2013. Decided appeals rose from 61,517, to 79,303 in the same period, a 29% increase that couldn't keep pace.

“Hence the big complaint that it’s taking forever for appeals to get resolved because the OMHA is overwhelmed,” said Mr. Blakeman.

“This is as bad as it’s ever been,” said Denise Wilson, assistant vice president of consulting firm AppealMasters of Lutherville, Md.

For Mr. Blakeman, the biggest impact on emergency physicians is “the injustice of it.”

“The audit process is broken,” he said. “Emergency physicians feel that you try to do the right thing for the patient but you can still lose your [Medicare] billing privileges if an auditor just has a bad day and picks you to unload all his or her mistakes on that day. It’s just not right. And the defense costs are unnecessary. We pay the cost of the federal audit process being poorly run.”

Richard Quinn is a freelance writer in New Jersey.