It leaves the project, dubbed Mercury 2, without a clear leader at a time when bricks-and-mortar retailers such as Woolworths are scrambling to restructure their supply chain and logistics systems to cope with the shift to online shopping.

Woolworths said Ms Coates, director of business transformation, had decided to leave the $45 billion retail group "to pursue other career opportunities".

Ms Coates, a 12-year veteran of the company, was the boss of its merchandise chain Big W between 2008 and 2013 and sits on the board of Woolworths loss-making hardware joint venture Masters.

It was only in October that Ms Coates took on the business transformation role, establishing the strategy and road map to overhaul its back-of-store operations that was expected to be a 10-year process and cost as much as $1 billion.

Woolworths heralded it as the next phase of its supply chain innovation and placed Ms Coates at the centre of a powerful working group that oversaw logistic operations that shifted more than 20 million cartons of goods each week and 3000 truck movements a day.

Mercury 2 is set to touch all of Woolworths' retail brands including its supermarkets, big-box liquor chain Dan Murphy's, Big W and Masters. The project is expected to set Woolworths up to be as nimble as possible in the wake of a massive shift by consumers to online shopping and away from its network of stores.

It is unclear who will replace Ms Coates as leader of Mercury 2, and if a new project leader will carry on with her strategy or present a new plan to the board.

Woolworths said Ms Coates would leave the company in coming months, but remain a director of Masters until the end of the year.

Woolworths chief executive Grant O’Brien thanked Ms Coates for her "significant contribution to the company over many years" on Friday and wished her well in her future career.

Ms Coates was a high school mathematics teacher in Melbourne before embarking on a corporate career.