Wellington rents jumped 9.8 per cent annually while Auckland's rose only 3 per cent, falling slightly last month, according to the latest Trade Me Property Rental Price Index.
Nigel Jeffries, head of Trade Me Property, predicted Auckland rents would rise this year.
Christchurch rents fell in the year to December compared to the previous year, the data showed.
Wellington was one of the strongest rental markets, with median weekly rents up by 9.8 per cent in the last year to equal the national median of $450, he said.
"Wellington started the year very quietly but took off in the second half of 2016. In the last 12 months there has been a $2000 increase in the annual cost of renting a typical property in Wellington," he said.
In Auckland, the December median weekly rent fell $10 to $510, but rents were up 3 per cent on the same time last year and Aucklanders could expect rent figures to bounce back, he said.
"Auckland has been very strong in the last few months and January is a very busy time in the Super City - we wouldn't be surprised to see the median weekly rent hit another record early in 2017," Jeffries said.
Nationally, rents for all properties rose 7.1 per cent from December 2015 to last month. In Christchurch, rents fell 5 per cent.
Trade Me compiles a rental price index which it says gives a comprehensive monthly insight into the market.
"The index is produced from Trade Me Property data of properties that have been rented in the month by property managers and private landlords. On average over 11,000 properties are rented each month and the report provides a comprehensive insight into this part of the property market for tenants, landlords and investors. The index is calculated using the median rent in the month, this being an accurate statistical assessment of the current rent being charged by landlords and property managers," Trade Me says.
Last week, the Auckland Property Investors Association warned that rent hikes could be more dramatic than in previous years as landlords look to pass on the cost of rising interest rates to their tenants.