Labor has attacked the Federal Government's decision-making process over funding for the Great Barrier Reef.

Under questioning in Senate Estimates, departmental officials revealed $444 million had been given to the Great Barrier Reef Foundation without it having to go through a tender process.

The funding is proposed to be given in one payment, which is the largest donation that any Australian Government has made to a single foundation for environmental projects.

Labor senator Kristina Keneally questioned why the funding wasn't allocated using a public grant process which was "competitive, open and transparent" so others, including the Great Barrier Reef Marine Park Authority (GBRMPA), could apply.

Senator Keneally said the foundation has six full-time members, and five part-time members.

In comparison, GBRMPA told the ABC it had 206 full-time equivalent employees.

The Great Barrier Reef Foundation idea was floated by a small group of businessmen at an airport waiting for a flight and set up in 2000.

The board is comprised of representatives of Australian business, science and philanthropy and is supported by companies including BHP, Qantas, Rio Tinto, Google and Orica.

The foundation is headed up by former Commonwealth Bank of Australia chairman Dr John M Schubert.

"The Government still can't explain why the money went to the foundation instead of being managed through the department or the Marine Park Authority, nor can it explain why the decision was taken without the foundation even being aware that it was being considered to carry out work on a scale completely beyond its historic capacity," Senator Keneally said.

Mr Birmingham told Senate estimates the foundation was best placed to do the work. ( ABC News: Matt Roberts )

The Federal Government has defended the process, with frontbencher Simon Birmingham telling Senate Estimates the foundation was best placed to do the work.

"The Government obviously did due diligence in relation to the foundation. It has a history of engagement with the foundation and believes the foundation is well placed to lead effort in this regard," he said.

Labor said the budget for the Great Barrier Reef Foundation would be increased 45 times, claiming its revenue for 2015 and 2016 was $9.6 million and $8 million respectively.

Queensland Environment Minister Leanne Enoch accused the Turnbull Government of failing to undertake due diligence in allocating its funding for the reef.

"The Government's inability to explain its decision making around a $444 million investment to just one single organisation is evidence of the absence of robust governance and leadership in managing the Great Barrier Reef," she said.

"For such a large investment, I would have expected more conscientious decision making."

The funding was announced by Federal Environment Minister Josh Frydenberg in April, with the money going towards water quality, tackling the crown-of-thorns starfish, and expanding reef restoration.

Mr Frydenberg said on Tuesday, partnering with the foundation provided an opportunity to "leverage funding from philanthropic and corporate sources" to complement the investment.

"While accessing their own expert advice, the foundation will also work closely with the Department of the Environment and Energy and the state government department as well as independent reef advisory bodies and expert institutions such as the Great Barrier Reef Marine Park Authority and Australian Institute of Marine Science to ensure the investment is delivered to best effect through a range of delivery partners," he said.

The Queensland Government said the Turnbull Government failed due diligence on reef restoration funding. ( Supplied: Christopher Tilt, Birds Eye View Drone Services )

Public servants may be seconded to help foundation

Ms Enoch said the Queensland Government was not consulted about the reef funding in the lead up to the federal budget.

Funding arrangements between the Federal Government and the foundation are still being discussed, but public servants may be seconded to the non-government organisation to help it roll out the funding.

Environment department official Dean Knudson said the department was liaising with the foundation.

"The Great Barrier Reef Foundation has been around since 2000, they've been active in the space of the reef and delivering programs on the ground," he said.

"This will be a significant scaling up of that organisation."

"There are opportunities where it makes sense to work collaboratively with the foundation. That could include potentially seconding staff that have experience in this area either in Great Barrier Reef Marine Park Authority, ourselves or Queensland to the foundation," he said.

Senator Keneally also questioned officials about the makeup of the foundation's members, but they would not comment.

The Great Barrier Reef Foundation has also declined to comment.