It comes nearly three months after the star disappeared from the public eye.Ms Fan, who is one of China's highest paid actors, will escape criminal charges if the fines are paid on time.
Axar.az reports citing Xinhua.
The actress had been linked to a government probe into how celebrities reported earnings in their contracts.
Some film stars were alleged to have used so-called "yin-yang contracts" - a practice where one contract sets out an actor's real earnings, and another details a lower figure, with the latter submitted to the tax authorities.
Chinese authorities have now ordered Ms Fan and the companies she controls to pay around 883 million yuan ($129m) in taxes, fines and penalties.
On Wednesday, the star posted an open apology on her Weibo account saying: "I've been suffering unprecedented pain recently… I'm so ashamed of what I've done. Here, I sincerely apologize to everyone."
Ms Fan's agent has been detained by the police for further investigation. Her studio had previously said the star never signed "yin-yang" contracts.
The 37-year-old actress, who appeared in the X-Men and Iron Man film franchises, sparked concern among her millions of fans when she disappeared from public view in June.
Social media was awash with speculation over her whereabouts and whether she had been detained.