The impact of the corruption case could be significant in New Jersey and involves one of the state’s most formidable, if aloof, figures.

Mr. Menendez won his first election, to the board of education in Union City, at age 20, and served six years as mayor before being elected to the House of Representatives in 1992. He was appointed to the Senate seat in 2006 by Jon Corzine, a Democrat who had vacated the seat to become governor. While he entered politics as a reformer, Mr. Menendez became known early on as one of the most effective machine players in Hudson County, which is heavily Democratic.

On Friday, Democratic leaders in the state took to the phones to plot how, as one put it, “to move a lot of the pieces around the board unexpectedly” should Mr. Menendez step down. Even as they did so, they cautioned against counting out a man known as one of the most tenacious political fighters in a state famous for them. But Mr. Menendez is also one of the least wealthy members of the United States Senate, and may not have the resources for a protracted legal fight.

Republicans called for his immediate resignation.

The federal investigation began with a salacious tip — unproven and vehemently disputed by Mr. Menendez — that Dr. Melgen had helped pay for under-age prostitutes for the senator in the Dominican Republic. The women who made the accusations ultimately recanted, but the Federal Bureau of Investigation continued its inquiry.

It shifted its scrutiny to the senator’s relationship with Dr. Melgen and whether he had traded gifts for favors from the senator. In January 2013, federal agents raided Dr. Melgen’s offices in South Florida. He, too, has denied doing anything improper.

Dr. Melgen was in the midst of a billing dispute with the government over his reimbursement for Lucentis, a costly medication used to treat macular degeneration, when Mr. Menendez contacted the Centers for Medicare and Medicaid Services.

The court papers that were mistakenly unsealed also revealed that a grand jury in New Jersey is looking into gifts that Dr. Melgen gave Mr. Menendez, in addition to the Medicare issue, as well as a deal Dr. Melgen had to sell port-screening equipment to the government of the Dominican Republic.