Payne had criticised the fact no World Cup games were scheduled for western Sydney next year.
Brown has come under fire because NSW received just two games in the tournament.
In a statement, he said: “The task of taking on two such senior roles – especially away from my home town of Melbourne – has been particularly stressful.
“The World Cup preparations are well advanced and I am very confident the foundations are in place for a successful tournament.
“The NRL has also put together a strong commercial team to take the game forward so this is an appropriate time to step aside.”