In a report released on Wednesday, the Australian National Audit Office said all decisions that led to the grant being awarded were informed by advice from the Department of Environment and Energy.
Guidelines were paired with the funding, as per commonwealth grant rules, and included "relevant and appropriate eligibility requirements".
But the auditor-general says the guidelines also had "two key shortcomings", being the level of detail provided on desired outcomes for the program and a lack of clear assessment criteria.
"The approach taken in the guidelines for this $443.3 million partnership grant did not enable an appropriate assessment of whether a partnership proposal represented value for money," the report states.
Labor environment spokesman Tony Burke said the report showed the foundation should never have been given the money.
"If elected Labor will be demanding all remaining funds and interest are returned in accordance with the contract," he said.
But Environment Minister Melissa Price says none of the findings affect the conclusion that the government's partnership with the foundation is an effective way to boost the health of the reef.
She says stopping or delaying the grant as Labor seeks to do will only delay the urgent increase in reef protection activities it will provide, such as improving water quality and tackling the Crown of Thorns Starfish.
"This is an investment we are immensely proud of; long-term funding to address the most urgent threats to the reef and to help manage further protection initiatives," she said.