"Boundary" explores the lives of people caught up in conflict in the area near the Preah Vihear temple, a flashpoint zone where sovereignty is currently under consideration by the UN's highest court.
It also shows scenes from Thailand's febrile recent history including a bloody crackdown on "Red Shirt" protesters in the heart of Bangkok in 2010.
Censors banned the documentary because "its content could cause a rift in international relations", an official at the culture ministry's video and film office told AFP.
The film could "cause disunity among Thais and jeopardise national security", he said, requesting anonymity.
Filmmaker Nontawat Numbenchapol vowed to appeal the ruling in a bid to have his documentary -- which made its screen debut in Europe -- shown in his home country.
"I'm very surprised my film was banned," he told AFP. "I'm preparing to lodge an appeal so it can be shown here."
Thailand does not dispute Cambodia's ownership of the 900-year-old Preah Vihear temple, a UNESCO World Heritage site that has seen deadly clashes along their joint border.
But both sides claim an adjacent 4.6-square-kilometre (1.8-square-mile) patch of land.
The Hague-based International Court of Justice (ICJ) completed hearings last week after Cambodia asked for an interpretation of the 1962 ruling on the Preah Vihear temple area.
A verdict from the ICJ, which judges disputes between states, is not expected for several months.
Thailand's bitter internal political divisions have led to other allegations of censorship, with a prime-time Thai soap opera axed suddenly this year amid accusations of government interference.