The lender, now part of Lloyds Banking Group, said house prices saw the largest increase in the annual rate of change in May, with a rise of 6.9%.
Prices are 8.3% above their April 2009 trough despite the decline over the past two months. The average house price is now £167,570; 16% below its August 2007 peak.
Last week Nationwide said house prices increased by 0.5% over the month in May and the annual rate of house price inflation dropped from 10.5% to 9.8%.
Stuart Law, chief executive of Assetz, said: “The discrepancy between Halifax and Nationwide’s figures can be put down to their small data sets.
"Halifax and Nationwide represent mortgages at the lower end of the market which are likely to have been the most affected over the last few years, impacting on their figures and the small volumes of transactions they record are leading to volatility in individual monthly data.”
Halifax cited the low supply of properties for sale as a key factor pushing up house prices in 2009, but the pickup in market conditions has encouraged more homeowners to attempt to sell their property.
The recent suspension of Home Information Packs and uncertainty about changes to Capital Gains Tax may also be persuading more homeowners to put their properties on the market, putting downward pressure on prices.
Martin Ellis, housing economist at Halifax, said: "The mixed pattern of monthly price rises and falls so far this year is consistent with a slowing market and is in line with our view that house prices will be flat during 2010 as a whole.
“The relative recovery in house prices in 2009 was driven by a boost to demand from reduced interest rates combined with a lack of properties for sale. These factors have lost some momentum in recent months. Further falls in the number of people in employment are curbing housing demand whilst the pickup in market conditions last year has encouraged more homeowners to attempt to sell their property."
Law has a more positive outlook on house prices.
He added: “As lenders continue to increase the number of mortgage products available and improve rates and loan-to-values, the market will continue to creep forwards and I would still expect to see a modest growth of 5% by the end of the year.”
