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, replacing the 11th and 12th teams which were automatically relegated. The third-placed team played the 10th placed Top League team, with the winner of that game taking a Top League place.
Two promotion/relegation matches (Irekaesen) were played with the winners qualifying for the 2004–05 Top League. The 10th-placed team from the Top League against the 3rd-placed team from Challenge 1. The 9th-placed team from the Top League against the 1st-placed team from Challenge 2.