The league has experimented with rotations limited to 80 in this year's NAB Cup pre-season competition and the league says there will be a restricted number in place in the 2014 season proper.
A number of clubs have complained that restricting the number of players off the interchange bench would lead to fatigue and could result in more injuries as a result.
But AFL boss Andrew Demetriou says the clubs need to get used to the new rule, although the number of changes involved has not yet been settled.
"With the cap, it obviously needs to be much higher," Jones said on Wednesday.
"I think it would be almost irresponsible to cap it at 80, if that's the figure that's being bandied around.
"It's going to come in and it's something that we have to get used to but I think they have to be really smart with the amount of rotations they allow a quarter."
Jones said it was clear that players would be under much more duress if they were required to stay on the ground longer.
"There's going to be a greater physical demand on the players, there's no doubt about that," he said.
"I haven't experienced it yet but the word from the players is that it's extremely tough, considering it's only been trialled in 20-minute quarters, whereas the season's quarters may go for 10 or 15 minutes longer.
"The demands are going to significantly increase."
Jones also backed the greater focus on concussion after two-time Brownlow medallist Greg Williams' recent revelation that he could not remember large parts of his career, which he put down to knocks to the head.
"Concussion is an interesting one to deal with, particularly as a player, because from the outside you look like you're 100 per cent and there's not much wrong - but there's just that feeling that you're not right in the head," Jones said.
"It's a tough one but with the head, you don't really want to mess with it because if the long-term effects are what they say they are, that can be pretty detrimental."