It was feared the issue might have ended up in the courtroom as Rugby League Central sought to bring agents under its jurisdiction for the first time.
The NRL, agents and Rugby League Players' Association (RLPA) have finalised a deal to adopt the new scheme.
At the heart of the issue was the game's inability to sanction agents for their part in the salary-cap scandals at Parramatta and Manly.
But under the new scheme, which will be managed by the RLPA, agents will come under NRL rules and may be banned if they are found guilty of wrong-doing.
All 109 agents signed up with none electing to opt out.
"Clubs will only be able to deal with accredited agents under the new scheme," NRL chief operating officer Nick Weeks said.
"Agents will come under the NRL rules for the first time, and that means agents will be held accountable in the same way as players and club officials.
"Equally, we hope this scheme will make our agents system more professional and that can only be a good thing for the game."
In a recent letter sent from the NRL to agents, the governing body confirmed it wouldn't reopen any disciplinary matters under the previous scheme.
Other changes include junior talent, who can sign with an agent from 15 years of age until they turn 17 and can terminate their agreement on three months' notice.
Senior players can also leave their managers without cause on three months' notice after an initial two-year period.
-AAP