In a statement she said her father's status as honorary president of the party "does not mean he can take the Front National hostage".
Last week she condemned her father for repeating his claim that the Nazi gas chambers were "a detail of history".
She is widely expected to run for president in 2017.
In the statement (in French), she says her father "seems to have entered a veritable spiral between a scorched earth strategy and political suicide".
"Given this situation, I have told him I will oppose... his candidacy in Provence-Alpes-Cote d'Azur," she said.
She said his "crude provocations seem aimed at harming me but, alas, they have dealt a very heavy blow to the whole movement".
The French media is now speculating on Jean-Marie Le Pen's possible ejection from the party he founded 40 years ago, the BBC's Hugh Schofield reports from Paris.
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Earlier this month Mr Le Pen, the party's founder, gave a radio interview in which he repeated his controversial remarks on the Nazi gas chambers, as well as saying the French wartime leader Marshal Petain was unfairly maligned.
He went on to say that France is governed by immigrants - singling out the Prime Minister Manuel Valls, who is of Spanish heritage - and that France needs an alliance with Russia to save the "world of the whites".
His daughter condemned those remarks, leading Mr Le Pen to declare to a far-right newspaper that "one is only ever betrayed by one's own".
Last month the FN polled 25% of votes in the first round of local elections.
While lower than some opinion polls had predicted, correspondents say that performance showed that Marine Le Pen's strategy, including shutting down the party's overtly racist elements, is paying off.
However, the party has faced a turbulent time in recent weeks, with the European Parliament calling in the EU's anti-fraud squad to investigate possible financial irregularities involving the party.
The head of France's far-right Front National, Marine Le Pen, has said she will move to stop her father Jean-Marie from standing in polls later this year.