In an open letter to Canadians released Monday, Commissioner Bob Paulson voices his frustrations over the process spelled out in the RCMP Act.
Allegations of widespread sexual harassment within the national police force surfaced last November.
The controversy was ignited by Cpl. Catherine Galliford, a high-profile 20-year veteran of the force, who spoke publicly about her internal allegations of sexual harassment and abuse by former male colleagues.
The complaints prompted an investigation by the RCMP Public Complaints Commission, which has asked for public input into how the Mounties dealt with the allegations.
In his letter, Paulson is almost apologetic, suggesting his ability to discipline "bad apples" within the force is hindered by the Act.
"I am trying to run a modern police force with a discipline system that was current 25 years ago," Paulson wrote.
"Right now this framework limits my ability to ensure our members' conduct is properly managed and corrected or, when necessary, to see to it that the bad apples are sent packing."
Paulson added that some discipline cases are "bogged down in an administratively burdensome and bureaucratic decision-making process" and could take years to resolve.
"It's unsatisfactory that we have to continue spending your tax dollars to pay individuals that don't deserve to be in the RCMP," he added.
Galliford has filed a lawsuit against the Mounties, alleging she was sexually assaulted, harassed and bullied over 16 years.
Galliford, who was the spokeswoman on the Air India and Robert Pickton investigations, said in a November 2011 interview that she spent years being treated as a potential sexual plaything by some supervisors, being called "baby'' and repeatedly propositioned.
In March, a former Mountie, Janet Merlo, launched a class-action lawsuit against the RCMP in B.C. Supreme Court.
That court action alleged Merlo was subjected to persistent and ongoing gender-based discrimination by male members of the force.
Last month, Paulson told a Commons committee that the RCMP was conducting a nationwide gender-based audit, to examine policies as they relate to how engaged women are throughout the force and how those policies affect their advancement.