Coles is suing the tax office in an attempt to claw back $40 million it paid in fuel excise, in what could prove a timely top-up for the supermarket's coffers during its first year as an independent company.

In five separate applications filed with the Federal Court in Victoria, Coles says that between 2014 and 2017 it paid tax on about 107 million litres of fuel which was lost through evaporation or leakage before it could be sold to customers at its chain of Coles Express service stations.

Coles is chasing about $40 million from the ATO. Credit:Edwina Pickles

Coles argues that because the fuel was never sold, it should be considered to have been "acquired... in carrying on an enterprise" and therefore eligible for fuel tax credits worth about $40 million.

A Coles spokesman said the company was "seeking clarification from the court as to whether it has overpaid fuel excise in the past, in particular in relation to fuel volumes that have been subject to leakage and evaporation".