Education Minister Jason Clare ordered the review after accusations of political interference in grant funding allocation, most recently under the former coalition government.
Queensland University of Technology vice-chancellor Margaret Sheil led the review alongside two academic experts and released her final report on Thursday.
The report found the level of trust in the council had been "dramatically eroded" by ministerial interventions in the past 20 years.
The review provided 10 recommendations underpinned by the need for the minister of the day to exercise proper and necessary oversight of the guidelines and funding levels available under grants programs.
"The ARC chief executive officer should have the capability and expertise to oversee the administration of the grants program," the report said.
"Individual grants ... should not require approvals by the minister, but recommendations and approvals should be made by those best placed to judge the intrinsic merit of the proposals."
The report called for increased support for Indigenous Australian academics through better consultation and extra fellowship opportunities.
Recommendations also included reforms to legislate the council's role in underpinning and shaping the national research landscape and new arrangements for the appointment and conditions of the council's chief executive.
Universities Australia said a strong, trusted research sector was crucial in times of uncertainty.
"The panel has struck the right balance in limiting the 'ministerial veto power' for use only when national security is concerned, with an appropriate level of transparency," chief executive Catriona Jackson said.
"Australia is in a period of uncertainty. Our ability to navigate what's in front of us hinges on our capacity to undertake world-class research from tackling the energy transition to supporting AUKUS."
The report recommended parliamentary oversight be required where a minister intervened in a grants process due to a potential threat to national security.
The Australian Academy of Technological Sciences and Engineering welcomed the review's recommendation to optimise the grants process by introducing a two-stage grant system.
ATSE chief executive Kylie Walker said a streamlined grants process would allow researchers to spend less time writing grants and more time on solving challenges facing Australia and the world.
"The new approvals process will provide certainty that research proposals will be assessed by experts on their scientific and research merits," she said.
Ms Walker also called on the government to address dwindling research and development funding.
She said a broader review of funding arrangements, which should be equal to about three per cent of gross domestic product, was needed to bring Australia in line with its international competitors.
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