"The rules have been a bit more difficult for us this year ... and obviously they were introduced to change Formula One," said Brawn after Schumacher claimed his record sixth championship in Japan at the weekend.
Ferrari also won their fifth successive constructors' title.
"It's a common comment that the FIA (International Automobile Federation) support Ferrari and it's a clear example where there was a raft of rule changes which were not in the interests of Ferrari whatsoever," he added.
"So when some of our friends feel that the regulations are moving towards Ferrari all the time, I think they need to take a more objective view."
Formula One's governing body, the FIA, changed the regulations this season to spice up the sport after a controversial year of Ferrari domination and falling television audiences in 2002.
The measures included one-shot qualifying, mixing up starting grids, and a new scoring system with points on offer for the top eight rather than six.
Eight points were available for second place rather than six previously, narrowing the advantage of winning.
McLaren's Kimi Raikkonen -- who won just once -- remained in title contention right to the end of the season whereas Schumacher -- with six victories -- would have won before the last race under the old scoring.
"These regulations didn't help us at all. But if they are better for Formula One, then we will do our best within the regulations," said Brawn.
"It certainly made it more difficult in many ways and I think after a period we have got to see whether it is correct that a driver who only wins one race can compete for the championship.
"That was how it used to be, if you remember, and then it was changed because it was felt that wasn't the correct way."
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