The league's salary cap officer on Sunday accused Toulouse of "breaches of the general obligation of transparency and cooperation" in the 2021-22, 2022-23, and 2024-25 seasons.
Toulouse, who have won both the most French rugby titles, with 24, and Champions Cups, with six, have been punished for transfer dealings in the past. They received a suspended fine in 2023 and a two-point deduction for this season - although still top the table by 12 points.
Toulouse fired back last month that the salary cap rules are partially "illegal and inconsistent" and have proposed repealing several provisions. The dispute threatens to end up in the courts.
This season, the Top 14 salary cap is at 10.7 million euros (£9.3m), although it increases based on the number of French internationals at a club.
In 2024-25, half of the top-flight teams reported spending 99 per cent or more of their allowance, according to a report by the salary cap manager.
But while France's rugby economy is booming, with rising crowds and television rights, clubs are in a precarious financial situation.
In 2023-24, the combined operating deficit of Top 14 clubs reached 64.5 million euros, the worst since the Covid-19 shutdown. Ten out of the 14 clubs were in the red.