In Carterton the three-month average was down 0.7 per cent to $241,144. In South Wairarapa it was up 1.7 per cent to $330,353.
Nationwide, the average house price was up 5.3 per cent to $428,308.
In numbers of sales, Wairarapa bucked a nationwide trend of decreasing sales by selling one more house in September compared with August, 59 ahead of 58.
Nationwide there were 5653 unconditional sales in September, a fall of 6.3 per cent on August and an increase of 418 sales or 8 per cent, compared with the same time last year.
"The traditional rush of spring listings has not eventuated this year and the market is tightening as buyers face a limited choice," said Reinz chief executive Helen O'Sullivan. She says a shortage of new listings is causing buyers to make rapid decisions, lifting house prices.
Over the past 10 years September sales have averaged 2.2 per cent higher than August, indicating sales this September were weaker than average.
Although Wellington has seen a slight increase in values this year, up 2.3 per cent, the market has seen little movement in the past six months, not following the trend of the other main cities.