Prices for tenant-owned apartments (bostadsrätter) jumped up 8 percent last year, compared to 2011, while prices for single family housed crept up a more modest 2 percent.
In December, however, prices for both houses and apartments had fallen by 1 percent nationwide.
"After 2011's dip for tentant-owned flats, we saw prices went up for all of 2012, despite financial uncertainty, a large supply, and longer selling times," Peeter Pütsep, head of real estate agency Svensk Fastighetsförmedling, said in a statement.
Currently, the average price for a house in Sweden is around 2.1 million kronor ($323,400), while the median price in the Stockholm area is 3.8 million kronor.
In the Gothenburg area, houses cost 2.9 million kronor on average, the same as average house prices in Malmö.