New Zealand Hotel Council chief executive officer Rachel Shadbolt said the earthquake was a major driver of the price increases.
"They are [now] operating off such a low base of rooms. And for want of a better word, it's skewed the data somewhat."
The Hotel Council's own data, due to be released today, shows that in 2010 before the first earthquakes Christchurch had an annual occupancy of about 67 per cent for its 3700 rooms.
In 2011 occupancy shot up to 85 per cent as the earthquakes reduced rooms available at member hotels to just 850.
Ms Shadbolt said the World Cup had brought significant price increases, particularly in Auckland and Wellington around game days.
"But midweek ... it was very much business-as-usual rates. So they didn't sit on a high rate for the entire six weeks for the Rugby World Cup."
Because prices were driven by supply and demand, a 13 per cent average price increase did not necessarily reflect current hotel rates, she said.
Taupo's average price fell 4 per cent, but it remained New Zealand's most expensive destination at $158.
Queenstown was next dearest at $153, while Hamilton was the cheapest of the major centres at $107 a night.
The Hotels.com data shows hotel prices in New Zealand averaged $132, compared with $200 in Australia, $254 in London, and $338 in New York.
ROOM RATES
Average hotel rate change in 2011:
* New Zealand +13 per cent to $132
* Christchurch +32 per cent to $130
* Wellington +15 per cent to $126
* Auckland +9 per cent to $132
* Hamilton +13 per cent to $107
* Taupo -4 per cent to $158
* Queenstown -1 per cent to $153.