Rents could increase by 4.5 percent to 6.5 percent, the New Zealand Property Investors' Federation (NZPIF) says.
The figure was higher than Treasury's estimate of 1.5 percent over three to four years.
Owners of commercial buildings and rental houses will no longer be able to claim depreciation on their investments.
The budget also removed a 20 percent depreciation loading on new plant and equipment purchased after budget day.
The two depreciation measures were suggested in the Tax Working Group report and the subject of speculation going into the Budget.
Finance Minister Bill English and Revenue Minister Peter Dunne said the moves would help rebalance the economy toward productive investment and reduce the incentive for people to buy rental property purely for tax reasons.
Mr English expected the changes to have only a mild impact on rents.
Today, NZPIF vice-president Andrew King said changes to depreciation would cost around $24 a week for the average rental property.
Not all of the increase would flow through to rents but they were likely to rise by 4.5 to 6.5 percent, he said.
The increase in GST to 15 percent would also have a "minor inflationary effect on rental prices".
Auckland Chamber of Commerce chief executive Michael Barnett said the changes in the tax treatment of investment property invited a move towards productive investment.
"If we achieve that from this budget it will represent a game change we have needed for decades."
The budget also changed rules for so-called qualifying companies (QC) and loss-attributing qualifying companies (LAQC) from April 2011, so that both profits and losses flow through from them.
"Changes to LAQCs and QCs to make them flow-through entities for tax purposes will reduce the opportunities for tax structuring," Mr English said.
The budget also prevents property investors from using rental losses to inflate Working for Families from April 1, 2011.
