The national championships were set to be raced at Chisholm Links, with the course getting tested at the Otago championships earlier this month.
Athletics NZ had been waiting to see what was happening with the Covid-19 alert levels.
It released a statement late yesterday and said if Auckland remained in Alert Level 3, Auckland runners would not be able to travel. The Government is due to make an announcement on levels on Monday.
The event would still go ahead, but it would no longer be know as the national championships. All the other centre athletes outside Auckland will be able to travel.
Athletics Otago will look to put in place processes and systems with an emphasis on safety and there will be a limit on crowd numbers and competitors. Contact tracing, good hygiene practices and physical distancing measures will also be actioned.
If Auckland goes down to Level 2 next Wednesday the full championships programme will go ahead. The closing of entries has been extended to the end of Wednesday.
Dunedin runner Oli Chignell won the New Zealand title in 2018 and is keen to repeat.
