New South Wales chief health officer Dr Kerry Chant said it was up to the NRL whether it wanted its players to have a flu vaccination.
Queensland has told the NRL its players would need a flu shot to play in the state, leading to Gold Coast Titans pair Bryce Cartwright and Brian Kelly being stood down for refusing the jab.
However, while New South Wales health minister Brad Hazzard told the NRL to "stick to the deal" on Saturday, Chant said the flu vaccine was a matter for the league.
"We have not determined and reviewed the plan. It is really a matter for NRL as a workplace employer to consider their occ [occupational] health and safety obligations and clearly there will be ramifications for them," she told a news conference on Monday.
"It is in their best interest to exclude any flu-like illness amongst players because, according to their plan, any player that has any respiratory illness is not allowed to play and it potentially will take the whole team out.
"It's in everyone's interest to obtain the flu vaccination, but as I said it's a matter for the occ health and safety requirements for the NRL."
The NRL is planning to restart its season on May 28 amid the coronavirus pandemic.
Chant said New South Wales, where 10 NRL clubs are based, had given the league a broad range of principles.
"I'm aware that [the] Queensland chief health officer has indicated that that is a requirement for Queensland," she said.
"We have not specifically endorsed a particular NRL plan, we've given them the broad principles they need to comply with in terms of their occ health and safety obligations."