Plans need to be started now to save the Great Barrier Reef.

AAP

MEASURS to improve the water quality of the Great Barrier Reef have been discussed by a meeting of federal and Queensland government ministers.

The Great Barrier Reef Ministerial Council met in Brisbane on Friday - a day after the Federal Government committed an initial $50 million towards protecting the health of the reef as part of its $200 million Reef Rescue project.

The meeting included federal Environment Minister Peter Garrett, Queensland Environment Minister Kate Jones and Queensland's Primary Industries Minister Tim Mulherin.

Mr Garrett says it is a new era of cooperation between Queensland and the commonwealth.

"Now we'll be able to work more effectively together after identifying a range of significant issues that need to be addressed, so the reef can continue doing what it does for the regions of Queensland and the Australian tourism industry," Mr Garrett said.

"About $146 million will be directed to land activities which recognises nutrient and pesticide runoff (from nearby farms) into the reef as one of the most critical issues to address."

The grants will fund land management and farm groups in minimising runoff of agricultural chemicals and nutrients.

Other funds will go towards water quality research and monitoring and a program to work with indigenous people, as well as a regular reef report card.

Ms Jones says the Queensland government will work with farmers in reducing run-off.

"The main focus is changing the way farmers use their products such as fertilisers and how much they use on their crop," she said.