WAFL Council of Presidents spokesman Haydn Raitt has conceded the right of West Coast and Fremantle to form their own reserves competition with Port Adelaide and Adelaide.
But the WAFL won't budge on allowing stand-alone Eagles and Dockers teams to play in its competition.
Raitt vowed that the WAFL was a resilient competition and would bounce back if AFL players were taken out, even if it affected funding.
"If they wanted to take their players and play in a different competition out of State, we completely understand that because those players belong to them and they have the right to do whatever they want with them," he said.
"If they wanted to join a competition like that, the presidents would all shake their hands and shake the players' hands and say that is the best deal for you."
Raitt said the WAFL clubs had the constitutional right to block the entry of stand-alone West Coast and Fremantle reserves teams and remained opposed in principle to host club alignments.
He acknowledged that having AFL reserves players undertake regular interstate trips would cost money and that indirectly would cost the WAFL money in reduced royalties.
"That is one of the negatives if they take that road - that there will be some money taken out of WA football. But at the end of the day, there is not much we can do about that," Raitt said.
"We all agree it helps our profile by having them in there, but it doesn't help them become a better side by one or 2 per cent because they can't have their players playing together.
"The WAFL is resilient and if that happened all clubs would be on notice that we have to do the best that we possibly can.
"I think we would fight back and still make the WAFL a great competition as it is today."
WA Football Commission chief executive Gary Walton said exploring alternatives was part of the process the AFL clubs had to go through, but he remained confident all parties were committed to finding a solution within the WAFL.