Last season's rule change of allowing three overseas players on the field at any one time was altered for the 2009–10 season; one of the three overseas players must have already represented Japan, be currently eligible to represent Japan or eligible to represent Japan in the future.
Teams are allowed to field one player from the Asian Rugby Football Union (ARFU) outside the above restrictions on overseas players. That Asian player may have represented another country at Test, A or Sevens levels as long as that country is a Union member of the ARFU.
Last season the top six finishers automatically qualified for the national championship; however, this season the top four qualify, with the teams that finish 5th to 10th playing off for the remaining two Top League qualifiers.
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
Top four sides of the regular season competed for the Top League Championship (the play-offs were not sponsored for the 2009–10 season). The teams competing were Toshiba Brave Lupus, Sanyo Wild Knights, Toyota Verblitz and Suntory Sungoliath.
The Top League teams ranked 7th and 10th played-off for the right to meet the Top League team ranked 5th in the second round. The Top League teams ranked 8th and 9th played-off for the right to meet the Top League team ranked 6th in the second round.
So Coca-Cola West Red Sparks and NEC progressed to the second round.
The Top League team ranked 5th played-off against the winner of the teams ranked 7th and 10th, and the Top League team ranked 6th played-off against the winner of the teams ranked 8th and 9th. The two winning second round teams advanced to the All-Japan Rugby Football Championship.
So Kobe and NEC advanced to the All-Japan Rugby Football Championship.
Two promotion/relegation matches (Irekaesen) were played. The Top League team ranked 12th played-off against the Challenge 1 team ranked 3rd, and the Top League team ranked 11th played-off against the Challenge 2 team ranked 1st. The winners were included in the Top League for the following season.