In the wake of the Alex Rodriguez doping case, which drew accusations of unethical behavior by Major League Baseball’s top investigators, the league has fired some members of its investigative team and moved to restructure the unit.

“After the Biogenesis investigation, we made a decision that certain structural changes were necessary in order to have a more efficient and effective investigative unit,” Robert Manfred, the M.L.B. executive who oversaw the case, said Thursday. “Once we made structural changes, it resulted in the elimination of some positions.”

M.L.B. and its commissioner, Bud Selig, faced claims from Rodriguez’s lawyers that its investigators had acted inappropriately during the investigation. Among the accusations were that baseball’s agents had paid people thousands of dollars for information and that in one case, an agent became intimate with a witness.

But at the conclusion of the dispute, M.L.B.’s chief arbitrator upheld most of Rodriguez’s record suspension, barring him for the 2014 season and postseason. The arbitrator, Fredric Horowitz, wrote in his decision that the “charges of improper conduct” by investigators were “unfounded.”