Residents' complaints about dust emissions following the first grain shipment from a new $40 million loading facility at Bunbury Port have sparked an environmental investigation.

Last week, Bunge Resources began loading 18,000 tonnes of wheat from the facility, but used a woodchip conveyer dating back from 1976 for the loading instead of a conventional conveyor.

The Department of Environment Regulation visited the port last Friday to investigate after residents complained of seeing a thick haze of dust.

One resident told the ABC he thought the port was on fire, while another said her car was covered in a creamy dust.

The Department has since advised the Port Authority to consider ways to improve dust management.

In a statement, the Department said the Port Authority had been asked "to consider any methods to reduce and, as far as possible prevent, future dust emissions".

"When the Department has received this feedback, it will then inspect the newly constructed silos, conveyors and ship loader," the statement said.

Bunbury Port Authority CEO Kevin Shellack did not want to be interviewed but provided a written statement to the ABC saying that the authority was "working with the exporter and relevant local authorities on the dust emission incident last Thursday evening".

However, in an email to a resident and obtained by the ABC, Mr Shellack said the loading of the grain had "unfortunately exposed some deficiencies in terms of dust control".

"Bunge have advised the Port Authority that they have implemented a number of additional controls to minimise the dust emissions and will continue to undertake engineering improvements to the system prior to the next shipment of grain," the email said.

Bunge Resources promises improvements

Bunge Resources CEO Chris Aucote said there had been "teething issues" and several improvements would be made before the next shipment.

"We learnt there are a lot of ways we can do things differently, and also we need to make some further modifications to the ship loader to ensure that some of the dust emissions points that were exposed are covered in so that they aren't exposed to the elements," he said.

Premier Colin Barnett said it was important the matter was dealt with so there was no threat to the port.

"If there is a dust problem we need to look at it with the Operator and figure out better ways to reduce dust," he said.

"Proper investment in handling facilities can contain dust. The last thing we want to do is close the port in Bunbury."

Conservation Council Director Piers Verstegen questioned Bunge's decision to use a 1976 woodchip conveyor to load grain and said it did not bode well for the port's expansion plans.

"I think this really calls into question the proposal by the Port to starting other bulk materials such as coal, when they are already having dust impacts on the community," he said.

"It's not acceptable after what happened down in Esperance with lead dust to not be using best practice in dust control.

"We don't want Bunbury to turn into another dust affected town like Port Hedland, especially when coal is on the cards."

In 2009, the Esperance Port was fined $525,000 for contamination after elevated levels of lead were found in the blood of some residents, including children, and hundreds of birds died.