Establishing the championship competition is designed to lift the level of competition for teams in Mangonui, Bay of Islands and Southern Districts division one competitions.
The Southern Districts Premier competition will now be known as the Bayleys Northland Premiership, with no other changes of significance taking place.
NRU chief executive Alistair McGinn feels the changes will help bring Northland together while also creating a truly premier top division.
"It's a really healthy change for rugby in Northland," McGinn said. "We're trying to cater to all teams here, and the changes have come from the sub-unions suggestions - they asked, we listened.
"This set up is similar to what club rugby used to like in the early 2000s, which was a competitive and successful set up that flowed into the Taniwha team."
McGinn added the changes in time will mean teams involved in the Premiership have earned the right to be considered one of the region's top teams.
Teams in the championship who win promotion have the scope to align with another club for the following season, if they haven't done so already - in order to be more competitive and field a premier and reserve team in the Premiership.
A review of this new format will be undertaken after the 2018 season.
Bayleys Northland Premiership:
Wellsford, Otamatea, Waipu, Western Sharks, Mid Western, Hora Hora, Old Boys Marist, Kamo, Hikurangi, Mid Northern.
Bayleys Northland Championship - North and South Zone from the following teams:
Awanui, Eastern, Kaitaia, Te Rarawa, Panguru, Kaeo, Kaikohe, Kerikeri x2 teams, Otiria, Whangaruru, Pipiwai, City, Mangakahia, Ruawai, Tomarata, and the following combined sides - Kaihu/Southern, Moerewa/United Kawakawa and Ohaeawai/Okaihau