The high-profile federal raid on a South Florida ophthalmologist’s office was more about potential Medicare fraud than about U.S. Sen. Bob Menendez, a longtime friend of Dr. Salomon Melgen.

Joining FBI agents on the two-day raid at the doctor’s West Palm Beach eye center: a team of investigators from the U.S. Department of Health and Human Services, which investigates Medicare wrongdoing.

The FBI is separately examining the ties between Menendez, a New Jersey Democrat, and Melgen in a parallel corruption investigation launched last year, The Miami Herald has learned.

FBI agents are investigating the allegations of a shadowy tipster who claimed the doctor flew Menendez on his plane to the Dominican Republic.

Earlier this month, Menendez quietly sent a $58,500 personal check to Melgen’s company to reimburse the cost of two flights to and from the Dominican Republic, the senator’s office confirmed Wednesday.

The tipster’s most explosive charge: that the two allegedly hired underage prostitutes.

DENIAL

Menendez strenuously denied the accusation and blamed it on an election-year conspiracy involving the conservative website, the Daily Caller, which stands by its reporting.

“Any allegations of engaging with prostitutes are manufactured by a politically motivated right-wing blog and are false,” Menendez’s office said in a statement Wednesday, following the raid on Melgen’s clinics in West Palm Beach and two other South Florida locations.

The ethics watchdog group that brought the tipster to the FBI’s attention also suspected that a partisan, political motive underpinned the allegation about the prostitutes.

The information was pushed just months before Menendez’s successful reelection in November.

What has transpired since is a web of political recriminations, big money, sex, hard-ball investigations and a public-relations nightmare for a powerful politician and his longtime friend, Melgen, who couldn’t be reached for comment.

BOXES AND BOXES

The raids on Melgen’s eye centers involved dozens of agents with the FBI and HHS’s Office of Inspector General hauling away boxes of financial documents, patient records and other materials that will be used for their joint Medicare fraud investigation into the doctor’s business.

In South Florida, the two agencies routinely join forces to investigate allegations of fraud, such as false claims submitted by healthcare providers to the taxpayer-funded Medicare program for the elderly and disabled.

Agents began their raid late Tuesday and continued their search into Wednesday at the doctor’s West Palm Beach office. At one point Wednesday, agents escorted a locksmith onsite.

BILLING

Agents conducted the raid primarily to investigate possible fraudulent billing activities by Melgen’s business. But they could use any evidence they find for the parallel corruption investigation concerning the prostitutes, trips Menendez took on the doctor’s private plane and the senator’s gift disclosures.

Menendez’s office said he flew only three times on Melgen’s plane: two personal trips in August and September of 2010 that did not need to be publicly reported and a May 2010 trip that was reimbursed by the Democratic Senatorial Campaign Committee, which Menendez chaired at the time.