The data published by Eurostat, the official statistical office of the European Union, also shows that on a quarterly basis prices were down 0.6% and 0.7% respectively.
The highest annual increase in house prices in the third quarter of 2013 was in Estonia with growth of 11.1% followed by Luxembourg with a rise of 6.5% but for flats only, and Latvia was up 6.2%.
The largest annual fall was in Croatia where residential property prices plummeted 16.9%, followed by Cyprus where prices fell by 8% and Spain with a decline of 6.4%.
But a number of other countries have seen prices rise on a quarterly basis. Although Estonia saw the highest quarterly rise at 5.3%, prices were up quarter on quarter in Ireland by 4.1% and in the UK by 2.5%. On an annual basis they increased 3.6% in the UK and 3.7% in Ireland.
The largest quarter on quarter fall was recorded in Slovenia where prices fell by 4%, followed by Denmark with a decline of 3.3% and Romania where prices were down 2.4%.
The decline also slowed in Spain with prices on a quarterly basis down by just 0.8%, the same as in the second quarter of 2013 and much less than in the first quarter when they fell by 5.1%. The annual fall in prices 6.4% is less than it was in the second and first quarters at 10.6% and 12.8% respectively.
Portugal has also seen an improvement. Prices fell by 0.4% in the third quarter compared with a decline of 0.9% in the second quarter of 2013 and 3.2% in the first quarter of last year. This takes the annual decline to 2.9%.
Prices in France are also edging upwards. They fell 1.2% quarter on quarter in the first three months of 2013, by 0.2% in the second quarter and increase by 1.2% in the third quarter. That takes the annual fall to 1.4% compared to 1.9% in the second quarter and 2% in the first quarter.
Other countries seeing prices rise include Sweden and Iceland. In Sweden prices were up 1.8% quarter on quarter and 5.8% year on year. Iceland recorded a quarterly rise of 2.5% and annual rise of 6.1%.
But prices have been fluctuating in Norway. Prices were up 2.9% in the first quarter of 2013 but this fell to a rise of 1.1% in the second quarter and they fell by 1.4% in the third quarter. On an annual basis prices were up 7.4% in the fourth quarter of 2012, but this fell to 6.9% in the first quarter of 2013, to 4.9% in the second quarter and in the third quarter the annual rise was just 2.1%.