House values in Whanganui were up just three per cent from 2007, compared to 29 per cent in New Plymouth, Mr Goodall said.
"There's continued to be value growth since 2015, although that's flattened off in the last few months."
The median loss on each property was just $15,000, slightly lower than in Palmerston North and New Plymouth.
The results were from the second quarter of this year, ending in June.
Property Brokers' Philip Kubiak said the property market in Whanganui was good, with a number of properties receiving multiple offers.
"House prices and sales in Whanganui continue to be strong. We're not following the trend of some larger centres."
He said house prices had improved significantly over the last few years.
"Four, five, six years ago some investors and even homeowners would be taking a hit.
"I would agree with the improvement and in many cases we're seeing a big improvement."
Local properties were selling for about 20 per cent over registered valuations, Mr Kubiak said, and in some cases over the asking price.
Gisborne and Invercargill also had relatively high percentages of properties making a loss instead of a profit - 6.1 and 5.5 per cent.
Sales made at a loss in a number of rural districts were high - 48.6 per cent in Buller District and, closer to home, 13.8 per cent in Ruapehu.
Just over 22 per cent of properties in South Taranaki sold for less than the owners paid, and 15 per cent in Tararua.
Queenstown was the clear winner in the report - no properties there were sold at a loss.
Just 3.7 per cent of properties sold throughout New Zealand incurred a loss. The percentage was exactly the same in the first quarter of 2017.
Mr Goodall said the figures were likely not a major concern for owner-occupiers.
"If you're going to live in the house, then maybe you're not concerned about that so much."
District/city Percentage Median loss
Whanganui 10.7 $15,000
New Plymouth 1.8 $18,150
Palmerston North 1.3 $20,000
Auckland 1.8 $26,000
Wellington 1.5 $30,000
Ruapehu 13.8 Not available
Rangitikei 5.8 Not available