A drop in the number house sales continues to put pressure on prices, with increases everywhere but Auckland and Canterbury.
The Real Estate Institute's House Price Index rose 0.1 percent last month, with the annual growth rate edging up to 3.8 percent.
The seasonally adjusted national median price rose 5.2 percent or by $30,000 over the past year to $560,000, but fell 1.6 percent Auckland to $850,000.
Three regions fetched record median prices, including Waikato, Wellington and Marlborough, with strong rises in Gisborne and Hawke's Bay.
REINZ chief executive Bindi Norwell said the lack of housing supply continues to put pressure on prices in the majority of regions across New Zealand, with 12 out of 16 regions seeing a price increase since June last year.
"Until we solve the supply issue, house prices are likely to continue rising, particularly as the OCR (official cash rate) remains low and the banks continue dropping interest rates," she said.
The volume of sales fell 5.4 percent in June, over May.