Prime Minister Malcolm Turnbull has been accused of making a "captain's call" over a controversial decision to give nearly half-a-billion dollars to a small Great Barrier Reef charity, after it emerged there were no departmental officials at a key meeting the Prime Minister attended.

Key points: The Great Barrier Reef Foundation was given more than $400m by the Federal Government

The Great Barrier Reef Foundation was given more than $400m by the Federal Government A Senate inquiry heard the offer was made at a meeting attended by the PM and the Environment Minister

A Senate inquiry heard the offer was made at a meeting attended by the PM and the Environment Minister Political opponents call it a 'captain's call' and say the PM should have sought departmental advice

In April the Federal Government announced it would provide the Great Barrier Reef Foundation with $444 million to fund projects to improve the health of the reef.

The foundation is supported by companies including BHP, Qantas, and Rio Tinto, and had six staff at the time it won the funding.

This week, at a Senate inquiry examining how the funds were awarded, the foundation's managing director Anna Marsden said the first time the charity became aware of the Government's intention was in early April at a meeting.

She said the meeting involved the foundation's chairman Dr John Schubert, Mr Turnbull, Environment Minister Josh Frydenberg, and the secretary of the Environment and Energy Department Finn Pratt.

"We were informed that there was an allocation being announced in the upcoming federal budget and they would like to invite the foundation to form a partnership with Reef Trust to distribute these funds," Ms Marsden told the inquiry.

The foundation's managing director said there weren't departmental officials at the meeting. ( Supplied: Queensland Museum - Gary Cranitch )

But later, in a letter to the inquiry, Ms Marsden corrected her statement.

"In the hearing I stated that the secretary of the Department of Environment and Energy, Mr Finn Pratt, attended the meeting with our chair on 9 April 2018. This is incorrect, Mr Pratt was not present in this meeting," the letter states.

The chair of the inquiry, Greens Senator Peter Whish-Wilson, said the absence of any departmental officials at the meeting was alarming.

"The process looks like a captain's call, it looks like a sham," he said.

"We've never heard of a process where the recipient of half-a-billion dollars of taxpayers' money gets it from the Prime Minister in a secret meeting without ever having asked for it in the first place."

Labor Senator Kristina Keneally also sits on the inquiry and said she was concerned there were no departmental officials at an important moment in the decision-making process.

"It also worries me that the Prime Minister seems to have gone into a meeting without any public service advice," she said.

"What advice did he have from the department that this was the right approach for the Great Barrier Reef?"

The Prime Minister's office referred queries about the meeting to Mr Frydenberg's office.

Mr Frydenberg defended the funding decision and said the Government had been "completely open".

"We provided a lot of this money to the foundation because they are able to leverage more funding off the private sector," he said.

"We have a comprehensive set of arrangements with the foundation to ensure that the Queensland [and] federal governments and the Great Barrier Reef Marine Park Authority are involved in the investment decisions and consulted, and indeed the foundation is made up of some of the most eminent scientists who understand the reef and the challenges it faces."

Senator Whish-Wilson said he would propose that the inquiry invite both Mr Turnbull and Mr Frydenberg to appear before it and answer questions about the Government's decision.