Stamp duty increases on high-end properties will discourage investment and reduce the supply of affordable rental accommodation, shadow treasurer Bruce Flegg has warned.

The top rate of duty on properties valued at more than $1 million increased from 4.5 per cent to 5.25 per cent this week, which will not only affect buyers in the market for a mansion, but also those investors who snapped up unit blocks and built multi-unit dwellings, Dr Flegg said.

"There are a large number of investors who buy small-to-medium-sized lots or an older apartment building," Dr Flegg said.

"Much of the lower cost rental properties will increasingly be in multi-dwelling situations ... this rise will add to the scarcity of rentals and the cost of renting."

However, a spokesman for Treasurer Andrew Fraser dismissed the claim and said investors spending less than $500,000 would pay less duty under the new rates.

From September, first home buyers will no longer pay stamp duty on properties costing less than $500,000, he said.

Mortgage duty has also been abolished in Queensland, which will benefit home buyers and investors taking out a home loan, he said.

"It is expected that the changes to transfer duty will result in a lower amount of duty being payable for a substantial majority of transactions," Mr Fraser said.

An increase in concessions and exemptions for home buyers will mean a reduction in duty payable on homes valued between $320,000 and $1 million.

However, Dr Flegg warned a number of investors would be hit by the increase, including small-time developers already struggling with construction costs and rising interest rates.

"I'm talking about the investment of building the stock of rentals... the development side of the industry."