The Australian equity market has underestimated the impact of the minerals resource rent tax (MRRT) on the valuation of companies, according to a Perpetual portfolio manager.

"The market has factored in a 5 per cent impact [on net present value]," Perpetual portfolio manager James Bruce said.

"My view is that the market is underestimating the impact.

"We are looking longer term and I think the market is looking two to three years forward. But I think it will drive significant changes to how mines are operated and run and the cost impact."

Despite the potential for the tax's greater impact, Bruce said he did not think the criticism from mining companies, particularly some of the smaller companies, was justified.

"I would like to think that some of the fearmongering that is going on by some of the companies is unjustified by the financial analysis behind it," he said.

"Now, our view is not that mines will close, just that they will be less profitable."

However, he did flag that an extension of the MRRT would pose a significant risk to investment in resource companies.

"The resources tax only applies to iron ore and coal and we are a bit surprised that it hasn't been a bit broader based than that," he said.

"I don't quite understand why it doesn't apply to copper, uranium and other commodities, but that is what the government has decided."

In earlier drafts of the legislation, the tax applied to a wider range of commodities, but the government decided the new resource tax would only apply to iron ore and coal, because they form, together with oil and gas, the biggest and most profitable commodities.

Oil and gas already have a tax in place.

But Bruce said there was the potential for an extension of the tax in the future.

"On a five-year view if you would look at risk in Australia, is it a possibility? Yeah. I don't think it is a high likelihood, but it is a possibility and there are some big projects in that [untaxed] space," he said.

The MRRT will commence on 1 July 2012.