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Across Otago median prices rose 5% to $420,000, while the Queenstown Lakes District was up 9.6% to again attain more than $1million, with the most growth seen around Wanaka.
Real Estate Institute of New Zealand (REINZ) regional commentator in Dunedin Liz Nidd said while Otago's sales count was down 12.2%, the market was otherwise "steady", with good buyer interest.
"We expect a strong run into Christmas with an increase in listing numbers and continuing strong buyer demand," she said.
ASB economist Kim Mundy said the lack of choice "crimped" sales figures in many regions around the country.
"The soft sales activity likely reflects a lack of choice rather than a weakening in demand," she said.
The REINZ's house price index rose 0.5% in September, or 4% higher than a year ago.
Ms Mundy said underlying demand was continuing to support prices, including in Otago, the Hawkes Bay, Gisborne, Bay of Plenty and Northland.
She predicted sales and median prices would remain "subdued" for the rest of the year.
Southland was one of the few regions to make gains in sales numbers, up 22.3% to 170 sold, while its median price rose 13.9% to $258,000.
REINZ regional director in Queenstown Gail Hudson said the area saw its "usual spring uplift" and posted a 9.6% price gain, compared with September last year.
"Most of the growth was driven by price increases in Wanaka," she said.
However, the sales volume was down 40% on a year ago, dropping from 70 to 42 houses.
She said low listing numbers in July had impacted on September, but there was a rise in listings in September and activity was expected to lift.
Of the 16 regions across the country, 14 areas made gains in median prices and four hit new records; Gisborne, 26.9% to $342,500, Nelson, up 23.1% to $592,000, Manawatu/Whanganui, which rose 18.9% to $321,000, and Northland, which rose 12.2% to $505,000.
Across the country 12 out of the 16 regions saw a decline in sales numbers, with six of those seeing double-digit decreases, with the national total falling from 5674 last year to 5506.
REINZ chief executive Bindi Norwell said that traditionally there was a six-week lag between significant movements in listings and sales results; July's listings having been at an all time low, which was reflected in September's low sales volumes.
"There simply weren't as many properties for sale, resulting in a very quiet start to spring," Ms Norwell said.
Now, the number of properties available for sale nationally had increased by 5.2% from 21,727 to 22,847, up by 1120 properties compared with a year ago.
Ms Norwell said that was the highest level of inventory for four months, and could drive sales this month and next.