The chart is compiled based on both physical and digital singles sales from music retailers throughout the country.
Happy has now been on the charts for 19 weeks and is also four times Platinum status, having achieved more than 60,000 sales.
The neo soul and funk single has also peaked at number one on charts in the US, UK, Australia, Ireland and 19 other countries, and was nominated for best original song at the Academy Awards last month.
Recorded Music NZ chief executive Damian Vaughan said records were made to be broken, but the Boney M single has had astonishing longevity.
"This certainly does mark a new era for the charts after the previous record held strong for so many years.
"The singles chart has always been a fantastic venue for pop culture," Mr Vaughan said.
"And the digital era and the internet certainly seem to have contributed to an explosive output of music which is probably contributing to the growing quality of productions."
The longest running number one album in New Zealand is Adele's 21 which sat at the top of the NZ Top 40 Albums Chart for 37 weeks.
Top 5 longest-running number one singles in NZ
1. Pharrell Williams - Happy - 15 weeks (2014)
2. Boney M - Rivers Of Babylon/Brown Girl in the Ring - 14 weeks (1978)
3. Scribe - Stand Up/Not Many - 12 weeks (2003)
4. Freddy Fender - Wasted Days and Wasted Nights - 12 weeks (1975)
5. Equal at 11 weeks: Katy Perry - Roar - (2013);
Robin Thicke feat. TI and Pharrell - Blurred Lines (2013);
LMFAO - Party Rock Anthem - (2011);
Smashproof feat. Gin - Brother - (2009);
Crazy Frog - Axel - (2005);
UB40 - (I Can't Help) Falling in Love with You - (1993);
Whitney Houston - I Will Always Love You - (1992).
