A controversial $444 million grant given to the Great Barrier Reef Foundation will be clawed back if Labor wins the next federal election.

But Prime Minister Scott Morrison says Labor will just use the cash to employ more bureaucrats in Canberra instead of helping the reef.

The coalition government has come under fire for granting the money to the small organisation without a competitive tender process, and now the opposition is calling on the foundation not to spend too much of the money.

Opposition Leader Bill Shorten said a future Labor government would demand any remaining funds be returned.

“We don’t think they should spend the money. We think that should come back and it should be reallocated much more professionally,” he told reporters in Townsville on Wednesday.

“Isn’t it an absurd situation where Australia’s leading scientists at the CSIRO now have to go to a charity run by ex-mining executives to be able to get money from the government?”

Labor’s environment spokesman Tony Burke said the funds should instead be spent on programs to reduce farm run-off, and go to bodies such as the CSIRO and the Australian Institute of Marine Science.

“A significant amount of it, you’d have to imagine, would go to the Great Barrier Reef Marine Park Authority itself,” Mr Burke said.

But Mr Morrison said distributing the money through the foundation ensured it was actually going to projects that help the reef instead of being wasted.

“We chose to invest in the Great Barrier Reef, and not doing it through a committee of bureaucrats,” Mr Morrison said.

“If Labor wants to pull the money back and employ more public servants in Canberra, well they can try that.”

A Great Barrier Reef Foundation spokeswoman told AAP on Wednesday the organisation had recently completed its plan, proposed projects, established a partnership management committee and an investment strategy.

The foundation maintains its “singular focus has always been delivering projects that protect and restore the reef for future generations,” it said in a statement on Wednesday.