The head of the CSIRO warned in internal emails that the Great Barrier Reef Foundation (GBRF) was in danger of spending "millions in overheads" after it received a controversial $444 million grant from the Federal Government.

The email was one of many revealed in documents tabled in Parliament this week, after Labor initiated an order for the production of documents.

The emails also reveal a string of other concerns by people within the CSIRO, including that the GBRF could have trouble showing it was spending the money well.

While CSIRO chief executive Larry Marshall was seeking briefings from colleagues ahead of a Senate estimates hearing in May, he revealed he had been in discussions with the foundation's chief executive John Schubert and managing director Anna Marsden.

He said Mr Schubert was "worried about navigating DoTE (Department of the Environment)".

An internal email within the CSIRO discussing the GBRF and the grant. ( Supplied )

Dr Marshall also said the CSIRO could help Mr Schubert with "more general management of the money", and continued to say: "Better we help than he burns millions on overheads."

The revelation comes amid continued debate over the Government's decision to grant the money to the GBRF without a competitive tender application.

Ms Marsden told the ABC last week she was surprised to learn the GBRF was getting the money — and that any due diligence conducted was done without their knowledge.

Sorry, this video has expired Anna Marsden on Great Barrier Reef Foundation's $444 million grant ( Leigh Sales )

The ABC revealed last week that some environmental lawyers believed the decision to hand out the grant broke government rules — a claim Environment Minister Josh Frydenberg strongly denied, referring to Department of Environment advice arguing the grant complied with the rules.

In another email tabled in parliament, a senior CSIRO business manager said the Federal Government's grant to the GBRF — in addition with another partnership with the Antarctic Science Foundation — "raises some questions", and wondered how the small charities showed impact from their funding "and not just photo-ops".

A 'political football'

The documents, tabled in the Senate after a request by Labor, also show the CSIRO was scrambling to get a slice of the $444 million grant, with another email saying Dr Marshall was "working on" Mr Schubert "in the background".

A reply email confirmed that was the case.

An email exchange between Peter Mayfield and Christian Roth.

"Yes indeed he is actively engaging John Schubert," an executive wrote.

On June 6, Angus Barnes, a business and development manager at CSIRO, wrote to Phillipa Ormandy, another business and development manager, forwarding an email that has been redacted, raising concerns with the grant.

Its subject was "Antarctic Science Foundation" — referring to another small charity, which the Australian Antarctic Division had partnered with.

"FYI … raises some Qs for me," Mr Barnes wrote.

"Along with the govt funding, going to the GBR Foundation — is this govt [sic] convened and supported corporate foundation model for environment a new thing?"

He also suggested they may not be good value for money, asking "how these orgs show true impact from their funding (and not just photo-ops)".

The emails also reveal the CSIRO attempting to please Mr Frydenberg by diverting attention away from particular issues about the foundation in Senate estimates hearings.

In one email, chief operating officer of CSIRO Hazel Bennett told Dr Marshall they should focus on what they could achieve with the foundation.

Ms Bennett wrote: "For tomorrow's meeting, I think we need to show that we have a prepared narrative on GBR — the minister's interest will be to see that we can navigate away from other hearing discussions about the independence of the foundation, and their appropriateness to receive the funding. Therefore our aim should be to keep focused on science and collaboration. Suggested messages below…"

The CSIRO also declined an ABC request for an interview on the topic of the grant, with the documents revealing that was partly because the issue was a "political football".

Sorry, this video has expired The PM has defended the Government's commitment of over $440 million to the Great Barrier Reef Foundation

GBRF defends track record in project delivery

The order for production of documents included documents held by the CSIRO and the Australian Institute of Marine Science (AIMS). So far, only the CSIRO documents have been tabled, with AIMS arguing complying with the order would be too onerous, since it found at least 23,000 relevant documents.

The CSIRO said in a statement to the ABC that it had a long history of working with partners on the reef.

"CSIRO has recently seconded a senior scientist part time to the GBRF to provide additional support on the design and process of the investment strategy for water quality improvement, as well as providing expert advice to the GBRF transition team on the Reef Trust Partnership program," the spokesman said.

"This scientist also leads CSIRO's GBR research efforts, and the secondment allows him to provide the GBRF with CSIRO's scientific expertise and deep domain knowledge on a range of reef matters."

The GBRF said to the ABC in a statement that it had a strong track record in project delivery, citing a number of examples, including some that were funded by the Federal Government.

When contacted for comment, Mr Frydenberg said the Government was investing in the reef.

"The Government's record $500 million investment builds on our $2 billion Reef 2050 plan to boost the health and resilience of the Great Barrier Reef," he said in a statement.

"The CSIRO and the GBRF enjoy a close working relationship and the foundation has made clear that science will drive all of its investment decisions."