FPS, owned by Lookers, had been the only UK-based member of ATR since 2004.
But after London-based ECP joined in May, FPS resigned because ECP is a customer and it fears a conflict.
FPS managing director Neil Davis said at its time of joining, ATR had only one member in each country outside Germany where it was founded.
He said: “This was important due to the unique position of FPS in the UK supply chain.
In recent years, ATR has changed this policy, appointing more than one member in certain European markets, including the UK.
“FPS has therefore decided it is no longer appropriate for it to be a member of ATR and has given notice of its resignation.
“This change will have no impact on FPS’s business in the UK.”
ATR said this appears to have been a misunderstanding.
A spokesman said: “ATR has long had an official policy of allowing more than one member per country. It would have been well known to FPS prior to them joining ATR in 2004.” ATR said ECP and FPS were not direct competitors, as FPS supplied factors whereas ECP supplied independent garages directly.