Four points for a win, two for a draw, one bonus point for four tries or more (BP1) and one bonus point for losing by seven or less (BP2).
If teams are level at any stage, tiebreakers are applied in the following order:
• Difference between points for and against
• Total number of points for
• Number of matches won
• Aggregate number of points scored in matches between tied teams
• Number of matches won excluding the first match, then the second and so on until the tie is settled
The top-placed regional teams from East Japan, West Japan and Kyushu played each other in Challenge 1. The top two were automatically promoted. The third-placed team played the 12th placed Top League team, with the winner of that game taking a Top League place.
The second-placed regional teams played each other in Challenge 2 for the right to play the 9th through 11th placed Top League teams, with the winner of each promotion/relegation match taking a Top League place.
Four promotion/relegation matches (Irekaesen) were played with the winner of each qualifying for the 2006–07 Top League. The 9th, 10th, and 11th placed team from the Top League played against the 3rd, 2nd, and 1st placed teams, respectively, from Challenge 2. The 12th placed team from the Top League played against the 3rd placed team from Challenge 1.