Prices in the ten areas with the highest numbers of empty houses were 15pc (£23,493) lower than the regional average, the mortgage lender said.
The number of empty homes is also aggravating Britain's housing shortage at a time when would-be buyers are struggling to get on to the housing ladder, Halifax said.
Stephen Noakes, mortgage director at Halifax, said: ''At a time when first-time buyers are still facing numerous obstacles to getting on the ladder, it is imperative we look further at the issue as an industry.''
Although the number of long-term empty private homes in England has fallen to its lowest level since 2008 - to 292,313 in April - this figure still accounts for 1.6pc of all private homes in England.
The North West has by far the highest number of long-term empty homes (63,696), accounting for over a fifth of the total across England.
It also has the highest number of long-term empty homes as a proportion of all privately owned properties at 2.5pc.
This is in contrast with southern regions which have a below average number of long-term empty private homes, with a low of 1pc in the South East.
Houses in places such as Pendle in the North West are trading at 29pc below the average house price in the region, due to the 4.8pc total of long-term empty homes there.
The number of long-term empty private homes rose in four of the nine English regions. The largest increase was in Yorkshire and the Humber (11pc).
Halifax housing economist Martin Ellis said that while it is encouraging that the number of long-term empty homes has decreased overall, it is still at a ''high level'' in the context of the country's housing shortage.
Communities Minister Andrew Stunell said the figures from the Halifax were based on council estimates, whereas the Government's own figures are based on firm council tax data and show the number of empty homes has fallen by over 21,000, the biggest drop since 2004.
However, he added: ''I am determined we do more to bring empty homes back into use to help tackle the pressing need for more homes in this country.''
