Mineral sands company Iluka Resources submitted a request to the minister in March, asking him to prepare an amendment to the Horsham Planning Scheme to allow for the disposal of low-level radioactive by-products.

The company wants to continue disposing of tailings at its former Douglas mine site once its Victorian operations cease this year. 

Iluka's formal request followed months of meetings between the company, Horsham, West Wimmera and Southern Grampians councils and government departments.

Horsham chief executive Peter Brown said council had not received official confirmation of Mr Wynne's decision, but had learnt of his request for Iluka to submit a planning permit to council after calling the department.

"We haven't been advised formally, but it does seem he is not going to consider an amendment application," he said.

Council will meet with Iluka today to discuss the company's next move.

Mr Brown said council would also seek a meeting with the state government. 

"The reason we refused it in the first place was we didn't think we had the resources or experience to manage it," he said.

Mr Brown said the advice council had received from government departments indicated asking the planning minister to assume control was the right way to go.

West Wimmera and Southern Grampians councils have backed Horsham's position, with West Wimmera writing to the planning minister in support.

Horsham Mayor Mark Radford said although the municipalities would be affected by Iluka's proposal in different ways, they stood united.

"If we are to become the planning authority we will have to make the decision, we won't be able to work together with the other councils anymore," he said.

"At the moment I'm saying 'if', because we need to find out more about it."

Kanagulk Landcare Group, which is concerned about radioactive material in pit 23 and possible contamination of groundwater - was disappointed council chose to refer the project to the planning minister.

Member Ian Ross told the Mail-Times in December he believed council had the relevant expertise.

"They have the most important qualification - they are local and they care,'' he said.

''They have empathy and the passion to support our community. The government departments have been somewhat arrogant.''

Mr Brown said the landcare group's concerns would be addressed regardless of who had planning authority.

Shadow Planning Minister David Davis said Mr Wynne had rebuffed requests from Resources Minister Lily D'Ambrosio's department and councils to take charge of the process.

"The minister has - at odds with the minister for resources - refused to play the requested role," he said. 

"He clearly doesn't understand the importance of this to the region."

Mr Davis said the technical nature of the decision was the reason councils had called for Mr Wynne's department to take responsibility.

He said the opposition had previously called on the government to establish a transparent process that would enable community input.

"Horsham council has obviously taken the view that it is a matter of regional significance and other councils supported them because of the technical nature of the decision," he said.

He called on Mr Wynne to visit the Wimmera to better understand the proposal.

Mr Wynne's office did not respond to request for comment before the Mail-Times went to press.