The federal Labor party is confident it will be able to scrap the Coalition's $443.3 million grant to the Great Barrier Reef Foundation if it wins the next election, even though tens of millions of dollars will have been already spent by the charity in its first year in operation.

While the Great Barrier Reef foundation chairman John Schubert and managing director Anna Marsden told a Senate committee inquiry on Tuesday they wanted to work with both sides of politics, the foundation is also looking at the legality of whether the grant can be revoked by a future Shorten government.