In October 2005, Flavell returned to New Zealand after a season with Japanese club Toyota Verblitz. In his last game for Toyota Verblitz in the 43rd Japan Championships on 12 February 2006 he was part of a team which lost to the top student side, Waseda University. This was the first time that a Top League team had lost to a university team.
He opted for a switch to the Auckland Rugby Union instead of joining his former union North Harbour (based in the northern part of the Auckland Region). He was contracted to Auckland for two seasons.
Flavell regained his All Black place in 2006 with two tests against Ireland before being injured for the rest of the season.
He was named captain of the Blues for the 2007 Super 14 season and was considered the outstanding forward of the Super 14, subsequently regaining his All Black Jersey. He played in the first five tests of the 2007 season. However he was left out of the All Black 2007 Rugby World Cup squad, being replaced by Sione Lauaki. Many people, including Zinzan Brooke considered this to be a bad decision.