One of WA's longest-serving football administrators has quit in disgust and will boycott this year's WAFL grand final in protest at the impact of the AFL alignment system.

Former WA Football Commissioner Brian Atkinson, currently the commission's returning officer and until recently the sole West Australian representative on the Australian Hall of Fame selection panel, resigned all his posts this week.

He told WAFC chairman Frank Cooper that the WAFL risked suffering similar damage to a decade ago when West Coast were aligned with East Perth and Fremantle were linked to South Fremantle. The Eagles are in the first season of a five-year arrangement with East Perth. The Dockers are aligned to Peel.

"My passion for and interest in West Australian football, extending over 60 years, has diminished significantly following the return of the aligned-clubs arrangements," Atkinson said in his resignation letter. "That did so much damage to the WAFL just over a decade ago, until the WAFC of the day threw it out as a failed experiment.

"Many of the current commissioners did not have to sit through the farce of that time which destroyed the WAFL as a fair competition and provided no improvement at all to the AFL clubs."

Atkinson, a former West Perth president and the club's historian, said he would miss his first WAFL grand final in more than 50 years in protest at the alignments.

He said East Perth's ninth consecutive win last week, which entrenched them in top spot on the ladder and strengthened their favouritism to secure the flag, was the final straw.

"It gets more depressing as the Eagles reserves juggernaut rolls on to its ninth successive victory - something East Perth has not been able to do for decades when left to their own resources," he said.

The West Australian

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