The government was warned that there was a “significant” risk that on-the-ground projects for the Great Barrier Reef could be delayed because of a $443.8m grant to the Great Barrier Reef Foundation, documents reveal.

The documents, obtained by the Guardian under freedom of information laws, also show the environment department and the office of the environment minister, Josh Frydenberg, discussing a $5m “reef islands” grant, but do not contain any mention of the much larger grant until after the 9 April meeting where it was offered.

According to the material, Frydenberg’s office was aware of the risks of the unusually large grant. “The rapid increase in operational scale for the foundation poses significant capacity, governance and capability challenges,” it states.

The information is contained in a set of preliminary “collaboration principles” for the grant that was sent by the minister to the foundation’s chair John Schubert on 22 April, after the $443.8m was offered.

Under a section entitled “risk management” the document states that challenges associated with the rapid increase in the small foundation’s operations could be managed through assistance from the Department of Environment and Energy and other government agencies and seconding staff to the foundation. But it notes this could delay on-the-ground work for the reef.

“The start-up phase could potentially delay delivery of on-ground projects, leading to loss of local capacity and momentum. The department has capacity to assist the foundation to implement transition arrangements while organisational capacity is being increased,” it states.

The Guardian had sought access to all correspondence between the department and the minister or his office relating to the $443.8m grant for the foundation. The department released seven documents in full and 35 documents in part but access was refused to 96 others including emails, talking points, letters and ministerial briefings on the grounds they would reveal deliberative matters in the department or were cabinet material.

The documents it partially released show that in the days before a 9 April meeting between prime minister Malcolm Turnbull, Frydenberg and Schubert, the department had been working on an application from the foundation for a $5m grant for a reef islands restoration project that was announced in early April.

On 4 April departmental staff sent a briefing note to Frydenberg recommending that funding be approved. Emails supplied for the week prior make no mention of the much larger $443.8m grant that was offered on 9 April.

In a 14 March document the department gave its assessment of the proposed reef islands partnership, but the documents supplied to Guardian Australia contain no due diligence work that the government says had been done by the department in March in relation to the almost half a billion dollar grant announced before the budget.

Earlier this week, Frydenberg said the government conducted two phases of due diligence as part of the grant process and that included the department seeking information from the foundation in March about its structure and operations.

However, the first emails that discuss the almost half a billion dollar grant in the documents supplied to the Guardian are dated 12 April.

Department emails sent on that day show that senior department officials, including the department secretary, Finn Pratt, and Dean Knudson, the deputy secretary for environmental protection, planned to meet with the foundation board members on 17 April and were in a hurry to provide a draft of the collaboration principles.

“The formal meeting with GBRF is being planned for Tuesday. It will be the secretary [Pratt] and Dean [Knudson] with a sub-group of the foundation board led by the chair,” reads email from Stephen Oxley, first assistant secretary for the heritage, reef and marine division. “The arrangements are being finalised by the secretary’s office.

“I am sorry for the breakdown in the provision of the information. We are jammed by the need to get legal review of the document combined with a timing imperative to get a copy to the GBRF to enable their internal discussion. My bad.”

Correspondence also appears to suggest that Paul Hardisty, the chief executive of the Australian Institute of Marine Science, was not made aware of the plan until days before the government’s announcement on 29 April.

An email from Deb Callister, assistant secretary in the heritage, reef and marine division, to senior colleagues on April 24 says: “A quick update on logistics:- · Paul Hardisty, CEO AIMS has been advised. He was very positive about the news – called it ‘elegant’.”

The documents provide little insight into who had the original idea for the grant or what internal discussions took place at a department or ministerial level before the 9 April meeting.

The government has been under pressure to reveal who had the original idea to award the grant to a private foundation, but has defended the process as transparent.

After questioning from Labor in the House of Representatives this week, the environment minister proffered a timeline of his decision making.

Frydenberg had said on Sunday that extensive due diligence had been done before the awarding the controversial grant. However, the managing director of the foundation, Anna Marsden, said on Monday she was unaware of that due diligence process and no one from the government had contacted her.

Frydenberg told parliament he took two submissions to the expenditure review committee of cabinet in March of this year, including one with “a proposal to establish a partnership with a non-government organisation, which was the Great Barrier Reef Foundation”.