Myhome.ie's figures show a 1.6% rise in prices in Dublin, which it noted is the first rise in prices in the capital in six years.
Daft.ie, however, registers a 0.5% drop in asking prices in Dublin.
It also points out that the stock of available properties for sale in Dublin is at its lowest level since 2007.
There are two potential reasons for the discrepancies. Daft.ie has a slightly bigger sample size. And the myhome.ie data are based on all properties listed on its website, while Daft's are only based on those properties listed during the quarter in question.
The Myhome.ie data reveals that the average property price in Dublin is now €240,000, 55% below their peaks in the fourth quarter of 2006.
It said that nationally house prices are continuing to fall but that the rate of decline is slowing. Countrywide house prices fell by 2.2% in the third quarter of 2012, compared to 3.2% in the second and 7.2% in the first quarter. It said that the average price of a house nationwide now stands at €207,000, 50% below their peak.
The rise in Dublin house prices was driven by fundamental laws of supply and demand, Myhome.ie's managing director Angela Keegan said.
''Our Dublin stock is down 20% from 5,960 to 4,780 in the space of three months and that kind of fall is something we have not seen in years,'' she said.
She also said the company had always maintained that any recovery in house prices would begin in Dublin, adding that that process is now underway.
''However, given the excess supply situation which exists in several parts of the country and the variable factors which will impact property prices in the future, the path to recovery is unlikely to run smoothly,'' she concluded.
The Daft.ie survey shows that the asking price of property nationwide fell by 3% in the third quarter of this year, down 14% from the same time last year. But it noted that there are large variations around the country.
Daft.ie said that in the three months from June and September, prices were mainly stable in Dublin were they fell by 0.5%. Cork prices fell by 0.6%, while in Galway and Limerick cities, prices fell by 2.6% and 3.7% respectively. House prices fell even further in Waterford, slumping 9.3%.
Outside the cities, Daft.ie also noted that asking prices in Munster saw their sharpest fall since the start of the property crash, with prices down almost 7% in three months.
''The latest report confirms that policymakers need to stop thinking of one national property market,'' commented Daft.ie's economist Ronan Lyons. ''Conditions vary dramatically between Dublin, where the number of properties for sale is at its lowest point since early 2007, and large parts of Munster and Connacht, where stock for sale remains very high,'' he said.
''This is seen in activity levels, also, with over half of Dublin listings sold or sale agreed within three months, compared to one quarter in many parts of the country,'' he added.