Farmers are facing new restrictions on the use of a weed killer conservation groups say is doing significant harm to the Great Barrier Reef.

Australia's chemical regulator has ordered a suspension on the use of diuron this wet season in situations where the chemical could be washed onto the reef.

But groups including WWF say it's already been found 60km inside the Great Barrier Reef Marine Park and the chemical should be banned outright.

The new restrictions, announced by the Australian Pesticides and Veterinary Medicines Authority (APVMA) on Monday, acknowledge diuron as a threat to aquatic ecosystems.

The regulator has acted ahead of a United Nations monitoring mission, due to arrive in March, to assess threats to the World Heritage-listed marine park.

In September, scientists from Queensland's Environment Department found traces of dangerous pesticides at up to 50 times the levels deemed safe in waterways flowing onto the reef.

Three chemicals, including diuron, were at toxic levels exceeding national standards for contamination of freshwater ecosystems at eight sites along the Great Barrier Reef coast.

The APVMA said the suspension was aimed at addressing the risk of diuron runoff into waterways.

"This includes uses that have high application rates or are applied on tropical crops during the wet season," the APVMA's Pesticides Program Manager Dr Raj Bhula said in a statement.

The regulator said it was continuing to consider diuron's effects, including monitoring results from Reef Rescue initiatives.

A final decision on the ongoing use of diuron is yet to be made, but Dr Bhula said further regulatory action was likely.

The suspension took effect on Monday and will apply until March 31 next year.

It bans the use of diuron on tropical crops - such as sugarcane, tea, bananas and pineapples - during the defined no-spray period in irrigation channels, drains, industrial and non-agricultural situations.

New usage instructions are being issued for the suspension period, including additional restrictions designed to minimise run-off, the APVMA said.

Possession and use in certain situations can continue provided diuron products carry the new instructions for use, it said.

WWF has long been calling for diuron to be banned entirely, and called the environment department's report in September a "smoking gun".

The APVMA been reviewing the use of diuron since 2002. In the meantime use of the chemical has been allowed to continue despite interim findings of unacceptable risks it poses to seagrass and dugongs in the Great Barrier Reef Marine Park.