In the last two quarters, house prices had gone up "substantially'' in Auckland, Mr Nagel said.
He said the figures meant affordability had not changed in the last three years for those wanting to buy in Wellington.
"It means that capital gains have been zilch in the last three years.''
The figures also revealed inner city living in the capital was being snubbed, with prices of some apartments down by between five and 10 per cent.
Mr Nagel said the Canterbury earthquakes had had an effect as buyers in Wellington were wary of paying for an older building that could be in need of earthquake strengthening.
He pointed to the sale of the 1905 Edwardian Albemarle hotel in Ghuznee Street.
It had a rateable value of $1.45 million, but a local newspaper reported it was passed in by the auctioneer when the top bid reached only $650,000.
National Comparisons:
* Ashburton District up 4 per cent since 2009;
* Hamilton city down 1.1 per cent over the same period;
* Christchurch up 3.3 per cent since the previous peak in 2007;
* Wider Auckland area up 7.8 per cent since 2007;
* Old Auckland City 11.2 per cent above 2007 peak.
* When adjusted for inflation no area has reached the previous peak, with Old Auckland City the closest at -2.8 per cent.
Wellington by the numbers:
* average house value $550,000 (+0.7 per cent since 2009);
* average unit $370,000 (-0.5 per cent since 2009); and
* average apartment $401,000 (-2.7 per cent since 2009).