The court in Turin ruled last month that the woman saying "enough" to her colleague who allegedly attacked her was not a strong enough reaction to prove she had been sexually assaulted.
The alleged victim is now facing charges for slander, reports said.
The ruling has caused outrage in the country.
"Certainly, you cannot punish the personal reaction of a woman terrified by what is happening to her," said opposition MP Annagrazia Calabria.
Justice Minister Andrea Orlando has asked ministry inspectors to begin looking into the case, which was examining incidents that took place in 2011, Ansa news agency reported.
The alleged victim, who worked in hospitals in Turin, said the defendant had forced her into sexual acts and threatened to stop providing her with work if she did not comply, the Corriere della Sera newspaper reported (in Italian).
Asked why she had not reacted to the alleged assault more strongly, she told the court: "Sometimes saying no is enough but maybe I did not use the force and violence that in reality I should have used, but that is because with people who are too strong, I just freeze."
The woman had been a victim of repeated abuse as a child by her father, prosecutors said during the trial.
Acquitting the defendant, the judge said the woman had not "betrayed the emotion that a violation of her person had to inspire in her", described her account as "unlikely" and said the assault "did not exist", Corriere della Sera said.
The defendant admitted sexual encounters with the woman but said they had been consensual.
Italy's justice minister has said he will investigate after a court acquitted a man of sexually assaulting a woman because she did not scream.