It has been almost two months since Auckland, Counties-Manukau and North Harbour have played in the competition because of Covid-19 restrictions.
The decision comes after government declined New Zealand Rugby's third travel exemption application to get the teams out of the region.
The NPC season will continue with the 11 provincial unions outside of the Auckland region, and NZR has confirmed there are plans to set up a separate Super City Series for the three Auckland teams once they are able to resume playing.
Steve Lancaster, NZR general manager of Community Rugby said:
"We believe we had a compelling case to safely move our teams out of the Auckland region without undue risk to the public, but we know government are operating in a difficult and complex world due to Covid-19.
"We're really disappointed for our Auckland based teams. It is an extremely difficult time with a lot of uncertainty for everyone involved in those teams, but we're grateful the competition can continue for the majority of our teams. We know we aren't the only ones being affected by the current Covid-19 outbreak.
"We are looking at the option of holding a Super City Series which would provide some meaningful rugby for Auckland, North Harbour and Counties Manukau and some live rugby for fans and supporters in the region. We are working with the Auckland based teams and key partners on the feasibility of making this happen."
With the Auckland region operating under Covid-19 Alert Level 3 restrictions, teams within the region are currently training under strict protocols. NZR will provide details surrounding a Super City Series in due course.
The three teams were cleared to resume training in a restricted capacity just over a week ago.
The Auckland, Counties-Manukau and North Harbour women's teams withdrew from the Farah Palmer Cup competition last month because of their inability to train or play under the Covid alert levels.