Millbrook Resort in Queenstown was rated the best hotel or apartment with a score of 4.74.
Wotif Australia and New Zealand product director Donna Rodios said it was a close call between first and second positions.
"The popular descriptive words used in the Wotif guest reviews of Quest Rotorua Central, included 'perfect location', 'flawless service' and 'pristine', which is tribute to the hotel's great location and outstanding service," she said.
Taupo's Sacred Waters Luxury Apartments, with a rating of 4.60, was rated third best hotel in the country.
"We were ecstatic to receive the news from Wotif.com, as well as written notification we received a Bottle of Moet & Chandon in the post, which was a pleasant surprise," Mr MacPhee said.
"We constantly monitor customer feedback from an array of websites and knew that we always trend well on customer service feedback and this acknowledgement from our guests and Wotif.com makes all the hard work worthwhile."
Mr MacPhee said Quest Rotorua Central offered a fresh product in the Rotorua accommodation scene with an excellent CBD location.
"However, we place great emphasis on service - taking the time to talk to guests on arrival and when encountered through their stay. The time spent at check in, offering advice on things to do, where to go and where to eat is greatly appreciated by guests.
"The small frontline team all offer a genuine level of hospitality which offers a five-star personal service to guests."
Quest Rotorua Central was last month awarded a Certificate of Excellence from Trip Advisor.
