The Queenstown-Lakes District had a 22.9 per cent rise to 28,224, and Waimakariri was up 17 per cent to 49,989.
The Census taken on March 5 this year was the first since 2006, after the 2011 survey was postponed because of the February 22, 2011, quake.
Christchurch city's population has fallen from 348,456 in 2006 to 341,469 this year - a drop of 2 per cent.
The Canterbury region numbers have risen from 521,0832 in 2006 to 539,433 this year.
Government statistician Liz MacPherson said one of the surprises was that while Christchurch city numbers were predictably down, people "do seem to be staying in the Canterbury region".
Of the 10 areas with the fastest population growth since 2006, half were in the Canterbury region - the second-largest region in New Zealand after Auckland.
Eight of the 10 Canterbury territorial authority areas experienced population increases between 2006 and 2013.
The Census also showed that New Zealand gained 7000 people a year from migration between 2006 and 2013 - less than a third of the 23,000 gained annually between 2001 and 2006.
The total "usually resident" population was 4,242,048 this year, up from 4,027,947 in 2006, with just over one million in the South Island and 3.2 million in the North.