Tuttle had been under fire from some politicians after the comments by Syrian-Palestinian filmmaker Abdallah Al-Khatib, with some media reporting that Culture Minister Wolfram Weimer had sought to oust her from the job.
However, after a meeting of the board of the state-owned KBB, the company that runs the Berlinale, on Wednesday, Weimer's office said in a statement that it welcomed Tuttle's willingness to "continue her work."
Angry rows over the Israel-Palestine conflict have repeatedly rocked the Berlinale, held every February as Europe's first major film festival of the year.
This year, Al-Khatib's comments at the closing ceremony, accusing Germany of being complicit in "genocide" in Gaza, provoked outrage from some German politicians.
Tuttle also faced criticism for posing for a photo with some of the team behind Al-Khatib's film, "Chronicles from the Siege."
On Wednesday, Weimer said Tuttle had "put a great deal of energy into setting a new course" at the festival, which she has led for the past two years.
"I thank her for her willingness to continue on this path," he added.
"I welcome today's decision by the supervisory board to reaffirm its confidence in my leadership of the Berlinale," Tuttle said in a statement.
Weimer noted that the board of the KBB had laid out recommendations for "strengthening" the festival, including a new code of conduct.
"The board has issued several recommendations, which we will carefully consider," Tuttle said.
Controversy surrounded this year's Berlinale almost from the beginning, after the jury president, acclaimed German director Wim Wenders, responded to a question about Gaza by saying cinema should "stay out of politics."
His remarks triggered a heated debate. Award-winning Indian writer Arundhati Roy later withdrew from the festival and criticised his comments.
Tuttle received support from thousands of filmmakers after German tabloid Bild reported that Weimer was trying to remove her from the job.
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