Wellington had an OTP of 78.93 per cent and Auckland 78.74 per cent. In first place was Cairns with an OTP of 87.2 per cent.
Auckland Airport acting chief executive Anna Cassels-Brown was disappointed with the result.
"We're not excited about seeing ourselves at the bottom of any league table, especially on a measure of customer service like on-time performance which is really important to us.
"It's one that we monitor on a monthly basis and analyse quite deeply ... so it's definitely not something we like to see."
It was important to remember that many of the issues that caused flight delays were out of the airport's control.
"The task for us is to try and filter out those ones which are outside of our control ... and really focus in on the ones that are within our control and what do we need to do differently, or what do we need to invest, or what do we need to change to make sure it doesn't happen again."
Delays at Auckland Airport could occur for any number of reasons.
"If the fuel truck doesn't get there on time, if the gourmet catering service loads up the wrong food or not enough of it - there are so many different things that can cause a plane to be delayed."
Auckland Airport was currently spending about $1 million a day upgrading its infrastructure and Cassels-Brown hoped this would improve its OTP in 2017.
New Zealand's top-ranked airport, Christchurch, said in a statement that it worked closely with its airline partners and agencies to be as efficient as possible.
"Having a fully integrated terminal - domestic and international in the same building - helps that.
"We have also recently increased the number of 'swing gates' we have - gates which can allow an aircraft to arrive as an international flight and depart as a domestic flight without having to change gates. This supercharges efficiency, especially for airlines using the same aircraft domestically and on the Tasman."
Wellington Airport has been approached for comment.
Meanwhile, Air New Zealand was ranked the eighth most punctual airline in the Asia-Pacific region with an OTP of 79.2 per cent. That compares with first-placed Qantas Airways' 87.6 per cent.
Air NZ didn't make the top 20 list for the most punctual airlines in the world, which placed Qantas as fourth and Virgin Australia 14th with an OTP of 84.5 per cent.
In the low-cost carriers category, Jetstar Airways was ranked 19th globally with 73.7 per cent of its flights running on time.
The most punctual airline in the world was Hawaiian Airlines with an OTP of 89.9 per cent.
Air New Zealand said in a statement it was proud to rank in the top 10 airlines in Asia-Pacific for OTP and to again be the leader on this measure for domestic air services in this country.
"OTP is affected by many factors, with the most significant being environmental, so no two years are the same for an airline. Weather events like significant winter storms or high wind conditions plus natural events, such as earthquakes, have a significant impact on OTP."
The airline said further improving its OTP would continue to be a key focus for 2017.
The study was based on some 54 million flight records using full-year data from 2016.
