The effect of the Canterbury earthquakes is being strongly felt in Wellington's commercial property market.

New research from Motu Economic and Public Policy Research Trust and GNS Science shows the price on buildings labelled by the council as earthquake prone drops on average 45 percent.

Motu Senior Fellow Dr Arthur Grimes said there is a wide variation on how much prices drop.

"If you're declared earthquake prone you're enforced by law to have to remedy that building, to bring it up to an appropriate standard. Your rents may drop if people don't want to rent in that building."

Dr Grimes said what surprised researchers was that buildings that were found to be earthquake prone after they were bought, didn't see the same discount.

"Now why that's the case, we can't tell for sure but it may be that the buyers thought that they were sound, and it turned out that they weren't, maybe because they got an engineering report that said something different to what the council thought."