The head of a small Great Barrier Reef charity caught in the eye of a political storm wasn't aware the federal government performed any checks before handing over $444 million in taxpayer funds.

Great Barrier Reef Foundation managing director Anna Marsden says no-one from the government contacted her - or anyone else in the charity - about the due diligence checks.

READ MORE Reef foundation boss wasn't aware of grant due diligence

It was not until Ms Marsden was listening to a Senate inquiry into the grant that she learned of the process.

"I'm certainly told - and I heard department officials in the inquiry hearing say - that they undertook significant diligence on the foundation," she told ABC radio on Monday.

The government is under mounting pressure over its decision to grant the funds to the foundation without a competitive tender process.

Environment Minister Josh Frydenberg defended the process, saying there had been "extensive due diligence" to ensure the foundation was best placed to receive the funds.

Ms Marsden said the foundation learned on April 9 it would receive the money and "afterwards we had to do an application".

That was the day she and foundation chair John Schubert attended a private meeting with Prime Minister Malcolm Turnbull, Mr Frydenberg and his Environment Department secretary Finn Pratt.

"We had to certainly demonstrate value for money and our track record," she said of the retrospective application.

Ms Marsden said questions about the process were for the government to answer.

"We've been told time and time again that the process that we followed is an absolutely correct process. There's a Senate inquiry. There will be outcomes from that."

Labor continues to pile pressure on the government over the "dodgy" circumstances surrounding the grant.

"This deal, from beginning to end, has been an inappropriate and dodgy use of taxpayer money," senior Labor MP Tony Burke told the ABC.

"Every question that gets asked about this, the more the government answers them, the more dodgy the whole process becomes."

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Mr Burke is concerned the decision means CSIRO reef scientists might have to go through the foundation instead of the government for funding and normal methods of ministerial oversight will be undone.

Mr Frydenberg argues there's nothing unusual about the grant.

The grant was made to the foundation, a charity set up in 1999 following the first mass coral bleaching 20 years ago, as a single lump sum.

"The money is to be spent over six years. By giving it all at once, they have maximum leverage to enter into contracts and start providing the money as needed, as they meet their objective," Mr Frydenberg said on Sunday.

The foundation has just six full-time staff and there is no clear plan so far for how the money will be spent.

Labor has called for the grant to be handed back.

The foundation's partners comprise businesses like Qantas and BHP and institutions such as ANU and the federal Great Barrier Reef Marine Park Authority.