Nunez, the former employee, in February sued the Levinsons, who dispute all the claims he has made against them and continue to represent star players. But M.L.B. continues to believe Nunez is telling the truth.

“Major League Baseball turned over the information from Mr. Nunez regarding the Levinsons’ alleged conduct to the M.L.B.P.A. because it is the union’s responsibility to regulate agents,” the commissioner’s office said in a statement. “Despite numerous requests, M.L.B. was disappointed it was not given the terms of whatever settlement that was reached between the M.L.B.P.A. and the Levinsons, and M.L.B. became aware that the Levinsons would be allowed to continue to represent players.”

In a statement, the Levinsons called Nunez a “liar and convicted felon,” and said they had no knowledge of his criminal activities, and that Nunez’s affidavit to M.L.B. mirrors the “baseless claims he raised in his lawsuit.”

“As for M.L.B.,” the statement continued, “they have opposed a strong union and our advocacy for players’ rights for decades, so it is unfortunate but not surprising that they have found it convenient to jump on Nunez’s bandwagon.”

Club owners have an inherently adversarial relationship with agents, whose duty is to extract as much money as possible from teams for their clients. But the past two baseball commissioners, Bud Selig and Rob Manfred, were so troubled by the repeated allegations by former associates against the Levinsons that they took the unusual step — at least three times in the past six years — of providing the union with information tying the Levinsons to their players’ use of banned drugs.

In 2012, Nunez, then an employee of the Levinsons, took the blame for facilitating Cabrera’s drug use and trying to cover it up. Cabrera was suspended for 50 games, and the union barred Nunez from being an agent for life. He spent three months in prison for his role in referring players to a South Florida clinic, Biogenesis, that provided athletes with performance-enhancing drugs.