A Florida eye doctor facing corruption charges with Sen. Robert Menendez, D-N.J., was indicted Tuesday for health-care fraud, with prosecutors alleging he cheated the federal Medicare program while receiving payments of $105 million over six years.

The payments to Salomon E. Melgen continued for much of that time despite scrutiny by federal officials, highlighting vulnerabilities in the federal program for the elderly and disabled.

A federal grand jury indicted Dr. Melgen, a North Palm Beach ophthalmologist, on 46 counts of health-care fraud, alleging among other things that he filed false Medicare claims between 2004 and 2013, federal prosecutors said Tuesday.

The 61-year-old Dr. Melgen earlier this month had pleaded not guilty along with Sen. Menendez after being indicted in the corruption case. Dr. Melgen was released on $1.5 million bail in that matter. A lawyer for Dr. Melgen declined to comment on Tuesday’s health-care indictment.

Dr. Melgen had gained attention as Medicare’s top biller when Medicare released billing records a year ago that named individual doctors for the first time in three decades following a legal effort by The Wall Street Journal. Making the data public could make it more difficult for medical bad actors to operate as freely, according to health-care fraud and law-enforcement officials.