But already this year there has been 53 incidents, CAA figures show.
"These changes address the safety risks that modern unmanned aircraft pose to other airspace users as well as people and property on the ground," said CAA general manager of general aviation, Steve Moore.
Civil Aviation Rule Part 101 and 102 will also require operators who want to fly over people or property to gain consent from the affected individuals or property owners before they fly.
Operators who intend to fly over public spaces will also need to get permission from the landowner.
Those who cannot get consent from a landowner or individuals can still operate if they get an operating certificate from the CAA under Rule Part 102.
"These changes strike a balance between safety and enabling operations," Mr Moore said.
The exact number of unmanned aircraft operations in New Zealand is unknown, the CAA said, but it receives up to 50 enquiries a week relating to their use.
Any breach of civil aviation rules can lead to a fine, written warning, or prosecution by the CAA.
Transport Minister Simon Bridges said the changes would enable innovation and put New Zealand at the forefront of regulating a rapidly evolving industry.
"UAVs are increasingly popular in a wide variety of operations, including scientific research, agriculture, fire-fighting, film and video production, as well as search and rescue," he said.
"One key way the government can help promote the uptake of new technologies is to ensure there are no unnecessary regulatory barriers."
Aerial photographer Tim Whittaker said the new laws would be very difficult to police.
"It is basically going to give them authority to prosecute if people get stupid," he told AAP.
