Jackson, who has been involved in some coaching with the Bay of Plenty Union, said he hopes to continue his involvement in rugby after he steps back from refereeing in March.
"I feel extremely privileged to have worked as a professional referee for New Zealand Rugby over the last 10 years but I feel the time is right to finish and move on to something different but hopefully still be involved with rugby.
"I would like to thank Lyndon Bray and Bryce Lawrence for everything they have done for me and their support in making this decision. I think New Zealand refereeing is in a positive space with great leaders and fantastic young referees who I will miss working with," he said.
New Zealand Rugby national referee manager Bryce Lawrence said Jackson leaves a legacy as one of New Zealand's best.
"Glen changed the shape of refereeing in our country when he became the first top class player to become a professional referee through the player scholarship system. Glen brought rugby nous to refereeing, strong relationships with players and coaches both domestically and internationally, and he added so much to our referee team culture by being a great team man.
"Glen has had a fantastic career in rugby, after 25 years at the top level it is time for his wife Fiona and children Payton and Ella to have more time together and I thank his family for their amazing support which has allowed Glen to travel internationally and referee on the biggest stages."
Jackson will travel to South Africa this weekend to attend a SANZAAR referee camp and will continue to support the New Zealand refereeing group through to the end of March.