Sydney and Greater Western Sydney’s salary cap allowance will eventually be cut, but it’s yet to be decided how severe or when the adjustments will be made.
Fairfax Media reports the Giants will continue to be allowed to pay their players an extra 9.8 per cent above the salary cap, which equates to an extra $1 million on player spending.
For the Swans, all existing contracts, including Lance Franklin’s nine-year, $10 million deal, will be honoured.
But the AFL will instead compensate the Swans with a new rent subsidy system, which is available only to footballers earning less than the average players' wage.
The changes won’t be fully implemented for another three years.
But Malthouse said the New South Wales teams should be brought back to the same terms as other clubs right now.
“2017? What's wrong with 2016 or 2015," the Carlton coach said on Wednesday.
"The quicker we straighten it out ... so there's no spikes in someone else's salary cap for particular reasons or because you live here or whatever you do, the better.
"I can spend another hour on this."
The Swans will be allowed to pay Franklin his $10 million contract regardless of salary cap changes. Photo: Getty
Malthouse also took aim at free agency, claiming it added to the financial stresses at the smaller Melbourne clubs near the bottom of the ladder.
"It's already been compromised by free agency. Not many players are going to put their hands up to play for the bottom sides," he said.
"But sides in the bottom will lose players who want to play for the top sides. So straight away they get stronger, and the sides down the bottom get weaker."
It is believed the AFL will announce its revamped salary cap rules and wider equalisation policy ahead of the Australian Hall of Fame function on June 4, the night before outgoing chief executive Andrew Demetriou's final day at work.
“I take my Carlton hat off and put on a football person's hat ... what do (the small Victorian clubs) get? How do they get advantages? They don't," Malthouse said.
"If anything, they're disadvantaged all the way through.
"They pay more for their grounds and a whole host of things. And it's not even the clubs you worry about so much, it's the supporter groups."
The Swans last month stopped ongoing player contract negotiations until the new cost-of-living allowance rules were finalised.