The federal government will spend $150 million on a program to boost water quality on the Great Barrier Reef after a UN mission said the site should be listed as in danger.

The program will repair land in catchments that are dumping large amounts of fine sediment into rivers discharging water to the reef, smothering coral, killing seagrass and increasing pollution loads.

It’s part of a $1.2 billion spend on reef health previously announced by the Albanese government, which has promised to fight an in-danger listing for the site.

The recommendation to list the reef as a World Heritage site in danger came late last year. It was based on what UN experts saw when they visited Australia about a year ago, when the Morrison government was still in power.

The UN report took Australia to task for not doing enough to tackle the key threats of climate change, poor water quality and harmful fishing activities.

In announcing the program on Thursday, Environment Minister Tanya Plibersek said the $150 million would fund work including fencing, revegetation, grazing management of cattle, and structural works to stabilise gullies and riverbanks.

“Sediment can coat seagrass beds, it can kill off seagrass, it can affect the health and even be responsible for the loss of animals and plants that make our reef special,” Ms Plibersek told reporters in Townsville.

“By dealing with sediment we are of course restoring the riverbanks and creek banks that’s good for the land, and we are protecting the reef from one of the greatest threats identified for the future of the reef.”

She said catchments along Queensland’s coastline will be targeted, with funding allocated pending the complexity of each individual matter.

Traditional owners and Indigenous groups will help identify priority projects.

“What we’d like to see is land care organisations, traditional owner groups and others come forward with proposals that will make a significant difference to the quality of the water flowing into the reef,” Ms Plibersek added.

The program will be carried out in collaboration with the Queensland government, which is spending $75 million on its own water quality program.

Special envoy to the Great Barrier Reef, Sentator Nita Green, said the funding is pivotal in rectifying inaction over the last decade.

“We are taking the divisiveness and the debate out of this conversation…to make sure that we can invest in our land holders, in our farmers and our traditional owners to make such a big difference to the Great Barrier Reef for generations to come.”

In its report last year, the UN mission said Australia’s efforts were not sufficient to protect the reef’s outstanding universal values.

It found management frameworks, strategies and plans had not been fully implemented, particularly in relation to water quality and fishing.