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The championship was set to involve the top teams from the Northern, Central and Southern leagues.
Instead, a new one-off inter-regional competition, with teams from Central and Southern, will run in its place for the women's and men's teams that are able to play.
In addition, it is now confirmed that the remaining Chatham Cup semi-final and final will be moved to February 2022 due to the uncertainty around when semi-finalists North Shore United are able to play again.
New Zealand Football general manager Daniel Farrow was disappointed not to be able to run full national competitions but pleased teams able to play now could.
"We have worked with our clubs and federations through the lockdown to attempt to find a solution and left it as long as possible to see if we could play the National League Championship," he said.
"Unfortunately, yesterday's announcement (from the government) confirms it isn't going to be possible.
The National League: South Central Series will feature the six regional qualifiers in the men's (Cashmere Technical, Miramar Rangers, Selwyn United, Wellington Olympic, Wellington Phoenix Reserves and Western Suburbs) and four federation sides in the women's (Canterbury United Pride, Capital Football, Central Football and Southern United).
The women's competition will be a double round robin league for the four teams involved.
The men's competition will be a single round league for the six teams involved followed by a grand final featuring the top two sides.
In the men's game, the revised series won't have any bearing on OFC Champions League qualification, which is separately being discussed with OFC.