Ross Brawn is working with the FIA in a bid to address the penalty system after seeing Michael Schumacher's Monaco GP "destroyed" by an ambiguity.
Schumacher was given the all clear by Brawn to race to the finish after the safety car peeled into the pits on the final lap in Monte Carlo following an accident involving Lotus' Jarno Trulli and Hispania Racing's Karun Chandhok.
The seven-times World Champion then pulled off an audacious move on old adversary Fernando Alonso in his Ferrari at Anthony Noghes' corner to claim sixth place.
Although the pass was made after the first safety car line, as FIA rules allow, and there were green lights indicating racing could resume, the regulations also state if a race finishes under safety car conditions, the field shall hold position across the finishing line.
But after a review by the stewards - a four-man panel which on the day included 1996 World Champion Damon Hill - Schumacher was handed a 20-second penalty that demoted him to 12th.
Mercedes then initially declared their intention to appeal, only to withdraw a few days later as they appreciated they were unlikely to win.
"What has come out of it is that there was some ambiguity in the regulation," said Brawn.
"We read it one way, and Charlie and his stewards read it another way, and quite frankly you could see both cases.
"We told Michael to race, and Stefano (Ferrari boss Domenicali) told Fernando not to race, so it was a bit unfair.
"Fernando was being told not to do anything, and we were telling our guy to go for it, that he had a chance.
"It was unfortunate, and that's why we wouldn't have felt great about going to an appeal because Fernando was told he didn't have to race.
"But I think the penalty we received was something that could have been looked at. Because of an ambiguity it destroyed Michael's race.
"So the penalty system needs looking at in those circumstances because it was unfair.
"We're now in discussions with the FIA to try and find a better system."
Brawn, meanwhile, sees no reason why 41-year-old Schumacher will not be with Mercedes next season, despite his poor form to date upon his comeback after more than three years in retirement.
Asked whether he was hopeful of keeping the same driver pairing of Schumacher and Nico Rosberg, Brawn added: "There's no reason not to.
"We're pleased with the drivers, they're both enjoying themselves."
