In the second stage, the top four teams entered a knockout competition, with third place playing fourth place in one match and first playing second in the other, with home advantage being decided by final league position.
Nelson Suburbs withdrew from the competition, and Metro were relegated and had to play in a play-off series with the winners of a competition between the northern, central, and southern regional competition winners for a place in the 2001 league.
The play-off games between the three regional champions were played at Palmerston North during September 2000; the match between Metro and the winner of this series was played the following month at North Shore as the curtain-raiser to the 2000 league final.
Controversially, when Nelson Suburbs withdrew from the league, their place was offered not to Caversham, but to Tauranga City United, a new team formed by the merger of Tauranga City and Mount Maunganui.
Metro again finished last in 2001, but withdrew from the play-off series with the winners of the northern, central, and southern regional leagues.