West has held the CA role since 2008 and also personally coached recently retired great Anna Meares.
"As recently diagnosed with MND, the notion "it won't happen to me" is crap. Get involved, help find a cure. The next victim could be you," West has posted on Twitter.
A Cycling Australia spokeswoman said West had stepped down from his job as head track sprint coach.
Nick Flyger will act in the position until the track world championships next April in Hong Kong, she said.
West, who has declined to comment, will continue to be involved in the elite cycling program as an interim technical director for the sport's peak body, the spokeswoman said.