While the Teranet National Bank national composite house price index rose 0.9 per cent in June from the previous month, the report found prices down in Ottawa-Gatineau.
Prices in Ottawa-Gatineau fell 1.7 per cent compared with a year ago, Quebec City dropped 2.4 per cent and Halifax lost 2.5 per cent.
Nationally, the index increase came as prices were up in seven markets out of the 11 tracked by the index with gains of 3.1 per cent and 2.8 per cent in Hamilton and Montreal respectively.
Compared with a year ago, the index was up 4.4 per cent, the lowest gain in six months with large variations across the country.
Calgary gained 8.1 per cent compared with a year ago, while Hamilton added 7.3 per cent and Toronto and Vancouver climbed 6.1 per cent.
The index is estimated by tracking home prices using data from public land registries.