WA's environment watchdog has set itself up for a showdown with one of the State's richest men after rejecting his plans for an iron ore mine in a part of the Goldfields it had promised to protect.

The Environmental Protection Authority revealed yesterday that it would not assess plans by Polaris Metals to develop a mine at the Helena-Aurora Range, about 100km north of Southern Cross.

Polaris' parent company Mineral Resources, run by Perth contracting millionaire Chris Ellison, reacted angrily and said it would put up to 2000 jobs at risk.

The EPA's ruling brings to a head months of warnings that it would take a "presumption against" further developments in the so-called banded iron formations of the Mid West and Goldfields until the State Government honoured commitments to safeguard parts of them.

According to the regulator, the BIF ranges are some of the oldest and most ecologically sensitive landforms in the world.

They are home to rare plants and animals that in many cases are found nowhere else.

Its determination cited as reasons for not assessing the proposal the "serious and irreversible impacts to the integrity of landforms of the Helena and Aurora Range" and the "loss of conservation significant flora, vegetation communities and fauna impact to Aboriginal heritage sites".

Mineral Resources said the EPA had only looked at environmental factors and had taken no account of the economic benefits of the mine proposal.

A company spokesman said the Government had identified the area as available for mining in 2010, leading the company to develop its plans according to "very high" environmental standards.

Labelling the decision not to assess the proposal as inappropriate, the spokesman said Mineral Resources was disappointed with a move it believed would deny the public "the right to have their say".

A spokeswoman for Environment Minister Albert Jacob said he would be unable to comment until he decided on the EPA's recommendation.