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Meet the doctor who got $21 million from Medicare

Following a rare look into Medicare payments, one South Florida ophthalmologist has emerged as the program's highest-paid individual doctor.

In 2012, Dr. Salomon Melgen of the Melgen Retina Eye Center received $20.83 million from Medicare. On his website, Melgen, who has been practicing for more than two decades and graduated from a Dominican Republic university, claims to be the only Hispanic ophthalmologist in Palm Beach, St. Lucie and Martin counties.

Dr. Salomon Melgen
Mark Elias | Bloomberg | Getty Images
Dr. Salomon Melgen

While this payout is large, it's still a small fraction of the approximately $77 billion in Medicare payments that more than 880,000 distinct health-care providers received in that year.

Read MoreSliver of Medicare doctors get big share of payouts

Melgen's emergence as the federal health program's highest-paid physician comes amid a criminal investigation of Melgen's alleged excessive Medicare billing practices the Miami Herald reported. The paper added that Melgen is known to be a close friend of U.S. Sen. Bob Menendez, D-N.J.

According to a New York Times report Wednesday, Melgen is viewed as a generous campaign contributor whose close relationship with Menendez has been scrutinized by federal prosecutors. A spokesman for Menendez declined to comment on the federal data about Melgen's Medicare billings, the Times report said.

In a statement to CNBC, Melgen's attorney, Kirk Ogrosky, denied claims that Melgen defrauded Medicare, adding that Melgen provided a substantial amount of free services and drugs to patients who couldn't pay.

"At all times, Dr. Melgen billed in conformity with Medicare rules,'' Orgosky said. "While the amounts in the CMS data release appear large, the vast majority reflects the cost of drugs. The facts are that doctors receive 6 percent above what they pay for drugs, the amount billed by physicians is set by law, and drug companies set the price of drugs, not doctors.''

Melgen's office did not immediately return CNBC's request for comment.

—By CNBC's Katie Little