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West Coast and Fremantle will pay $450,000 a year each for alignments with East Perth and Peel respectively for the next five years under an historic agreement clinched this week by the West Australian Football Commission.

WAFL clubs were last night briefed on the agreement which was signed on Monday night by the Royals, Thunder, Eagles and Dockers. The agreement will start in 2014, although some players will shift clubs next season as part of transitional arrangements.

WAFC chairman Frank Cooper and CEO Gary Walton hailed the agreement as "coming out of the industry" based on guiding principles put to them by WAFL and AFL clubs.

Both said the agreement was the result of a more mature football industry and not comparable to failed arrangements in place with Claremont, South Fremantle and East Perth a decade ago.

"We have done a lot of work on this and referenced it back to the key objectives that the WAFL clubs and AFL clubs gave us at the football summit about the integrity, history of the WAFL being protected and improving the financial sustainability of the WAFL and giving the AFL clubs what they are after in terms of their players playing, training and being managed," Cooper said. "We think this delivers on all of those."

Under the agreement:

- The alignments must stay in place for a minimum of five years, with 20 months notice to be given to terminate even after five years

- The seven non-partner clubs will have their annual grants increased from $425,000 to $525,000. Of the $100,000 increase, $70,000 can be used in year-to-year operations, $20,000 must be put towards building assets and $10,000 towards improving technology

- Partner clubs will receive grants totalling $350,000. They are expected to make up the difference in saved recruiting costs, salary cap savings, coaching staff savings and medical staff savings

- The WAFC will establish an annual $350,000 development fund. The first target of that money will be to develop shared services between clubs to help slice running costs and improve sustainability

- AFL clubs will have the final say in appointing the senior coach of their aligned club, in consultation with the club. This is not expected to affect the appointments of Brian Dawson at East Perth or Cam Shepherd at Peel

- Peel and East Perth are to maintain their logos and names

- All Fremantle players at East Perth, and West Coast players at Peel, will be swapped to their aligned club for 2013

All interstate players selected in the 2012 national, rookie and pre-season drafts will also join the aligned club next year. The remainder of the AFL squads will join the aligned club in 2014.

┬ĚThe WAFC will retain the right to alter the recruiting and playing list conditions of the aligned clubs to make sure they are neither too dominant nor too weak.

"We have referenced it back to the key objectives that the WAFL clubs and AFL clubs gave us."