The number of rental properties on the market has halved since last year, which will probably mean stiff competition for places and increasing rents, according to Trade Me.
The shortage means in October the average rental attracted 28 percent more inquiries within the first week of being listed than a year ago, the online marketplace operator says.
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Wellington was hardest-hit with 69 percent less rental properties.
"Which is worrying news for those flat-hunting in the capital," head of property Nigel Jeffries said.
The national median weekly rent had remained unchanged for 11 months, at $450, and the supply and demand had remained relatively balanced in the last year, he said.
But now it appeared the scales were tipping.
"If this trend continues, things are going to be very tough for a huge number of renters, particularly students, who will be hunting flats in summer," Mr Jeffries said.
"Properties are getting snapped up fast as demand outstrips supply. A two-bedroom flat listed in Wellington recently received nine enquiries in its first three hours ... and this is just the tip of the iceberg."
The number of available rentals in Auckland dropped 35 percent and the median weekly rent increased 2.9 percent to $525.
"If this shortage of rental properties continues we can expect to see new record rental prices in the City of Sails," Mr Jeffries said.
Christchurch's rental supply dropped 59 percent. Although the median rent fell 1.3 percent to $395 per week it was "only a matter of time" before prices rose, he said.
In the provinces, Hawke's Bay, Nelson and Southland reached new record rents in October.