The House Price Index rose 3.1 per cent in the second quarter of the year compared to the first one, to 102.74, the highest since Q1 2015, the statistical service said.
Compared to the second quarter of 2016, house prices rose 3.6 per cent, Cystat said in a statement on its website on Wednesday.
In the first quarter, home prices rose an annual 2.4 per cent and dropped a quarterly 3 per cent.
The Cystat index relies on data obtained by the Department of Lands and Surveys. The Central Bank of Cyprus, which said in August that home prices rose in a quarterly 0.3 per cent in Q1, and 0.2 per cent year-on-year.
The Cyprus division of the Royal Institute of Chartered Surveyors (RICS) said that in August that house and flat prices rose a quarterly 2.3 per cent and 1.3 per cent in January to March.
In Q1, houses and apartments became 4.9 per cent and 3.3 per cent less affordable compared to the respective period last year, according to RICS.
The central bank and RICS apply a different methodology.