Prices increased 1.2% compared with the previous quarter. In the euro area, house prices rose 4% annually and 1.1% quarterly, Anadolu Agency reported.
Annual growth slowed from 5.1% in the EU and 4.6% in the euro area in the first quarter.
Portugal recorded the strongest annual increase at 16.5%, followed by Bulgaria at 15.5% and Lithuania at 14.3%. Finland, Luxembourg and France registered annual declines.
Other substantial annual increases included Slovakia at 13.6%, Croatia at 12.7%, Spain and Romania at 12.1% each, Latvia at 11.4% and Hungary at 10.2%.
Prices fell 2.7% annually in Finland, 2.2% in Luxembourg and 0.8% in France.
On a quarterly basis, Lithuania posted the largest increase at 5%, followed by Bulgaria at 4.5% and Romania at 4.4%.
Latvia recorded a quarterly rise of 3.9%, Portugal 3.6%, Estonia 3.5%, Spain 3.4%, Austria 3.3%, Slovenia 3% and Denmark 2.8%.
Hungary and France recorded quarterly declines of 1.4% and 0.8%, respectively.