Poitras filed the complaint in the District of Columbia under the Freedom of Information Act, demanding the release of records related to her detainment and questioning on various airports on more than 50 occasions.
The director is known for her work on politically sensitive topics, including her chronicling of America post 9/11 in her documentaries.
She made "My Country, My Country", a documentary on the American military occupation in Iraq, "The Oath", on the Guantanamo Bay prison and "Citizenfour", on NSA whistleblower Edward Snowden, which won an Academy Award for best documentary feature this year.
The director said she would get held up for hours at a time, would be told that she was on No Fly List, and had her electronic equipment held for 41 days. She was also threatened with handcuffs for taking notes while she was working on a film about Julian Assange and WikiLeaks.
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Poitras first filed an FOIA request in January last year and though the Department of Homeland Security, Immigration Customs Enforcement and the Transportation Security Administration have acknowledged her requests, they have not been responsive with documents.
"I am also filing this suit in support of the countless other less high-profile people who have also been subjected to years of Kafkaesque harassment at the borders. We have a right to know how this system works and why we are targeted," Poitras said.