The Paris prosecutor's office revealed that charges of "public insult and inciting hate" were filed in mid-November.
The charges stemmed from a legal action by a Croatian community group in France over the interview in Rolling Stone magazine. A lawyer for the group, Ivan Jurasinovic, said they only want Dylan to apologise to the Croatian people for the comments.
He did not say why they filed the case in France. The country has strict laws punishing hate speech and racist remarks.
Speaking about race relations in the United States, Dylan was quoted as saying: "If you got a slave master or Klan in your blood, blacks can sense that. That stuff lingers to this day. Just like Jews can sense Nazi blood and the Serbs can sense Croatian blood."
Mr Jurasinovic said the 30,000-strong Croatian community in France was upset by the remarks, but he did not know why Croatians in Croatia or the United States, where Rolling Stone is based, have not filed similar suits.
The charges were filed two days before Dylan received a French government honour at the Culture Ministry but were not publicly confirmed until this week.