The files, dating from 1954 to 2009, include drawings of flying saucers and alleged samples of alien writing. The files include details of New Zealand's most famous UFO sighting when strange lights were filmed off the South Island town of Kaikoura in 1978. An official report from the time said natural phenomenon could explain it.
Although the incident made international headlines at the time, the military report suggested it could be lights from boats reflected in clouds or an unusual view of the planet Venus.
Following the release of the files, New Zealand Air Force spokesman Kavae Tamariki said the military did not have the resources to investigate UFO sightings and would not be commenting on the documents' contents.
"We have just been a collection point for the information. We don't investigate or make reports, we haven't substantiated anything in them," he told the Dominion Post newspaper.
The reports have been released under freedom of information laws after officials removed names and other identifying material. The files - which run to about 2,000 pages - include accounts by members of the public, military personnel and commercial airline pilots describing close encounters, mostly involving moving lights in the sky. All the original documents on which the reports were based are to remain sealed in the national archive.