The third round of the season was cut short just after 75 percent distance following a huge crash at 130R involving the NISMO Nissan of Tsugio Matsuda and the JLOC Lamborghini of Kosuke Matsuura.
At the time of the stoppage, the NDDP Racing Nissan shared by Katsumasa Chiyo and Mitsunori Takaboshi was leading by virtue of being the only car in the GT500 field not to have performed its second mandatory pitstop.
The NDDP car was provisionally declared the winner, prompting a mass protest by rival teams that led to Chiyo and Takaboshi having one minute added to their race time - dropping them from first to fourth in the revised results.
Toyota squad Racing Project Bandoh and drivers Yuji Kunimoto and Sena Sakaguchi were promoted to victory, although this wasn't made official until a week after the race as NDDP lodged an ultimately unsuccessful appeal.
In the wake of the controversy, GTA chairman Masaaki Bandoh promised changes to the sporting regulations in time for the fourth round of the season, which takes place next month at Fuji Speedway, and these were published on Friday.
The new rules now specify that when a race is red-flagged and not resumed but has passed 75 percent distance, as was the case at Suzuka, any car that has not performed its pitstop obligations will be given a one-lap penalty.
However, it has also been clarified that if a race is stopped before 75 percent distance, the mandatory pitstop rule will no longer apply.
Any car that takes the chequered flag without having completed its mandatory stops will be disqualified.
In cases where one driver stays at the wheel of a car for more than two-thirds of the originally-specified distance in a race that is red-flagged and not resumed, a one-lap penalty will also apply.
One other minor amendment has been made to the rules concerning pitstops made under caution.
Teams are now allowed to make pitstops to change from dry to wet tyres for up to two laps after the introduction of a safety car period, to prevent teams from being forced to stay out on slicks on a wet track. No other pitwork is permitted during such stops.
This amendment follows several cars being caught out in a weather-affected opening race of the season at Okayama.
Additionally, the pitlane reopening after being closed under the safety car will now be staggered, so that GT300 cars cannot pit in until the lap after GT500 cars are allowed to pit.
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