John Aglionby, Jakarta – Freedom of speech in Indonesia has suffered a significant reverse after censors banned four "disturbing" documentaries on East Timor and Aceh from the Jakarta International Film Festival (JiFFest).

Tuti Said Sadikun, the censorship board's chairwoman, said that exposing the public to films about the independence struggles in the two territories might jeopardise relations with Dili and the peace process in Aceh.

The decision is likely to be seen as a regressive step by a government that seeks to project itself as a regional beacon of democracy and an advocate of freedom of expression, despite inconsistencies in application.

Analysts say it also shows that many influential people in Jakarta have not reconciled themselves to the humiliating loss of East Timor in a UN-sponsored referendum in 1999 and the government's decision to sign a peace deal in 2005 with the Free Aceh Movement (GAM) after a 29-year armed insurrection.

Ms Tuti said it made no difference that the films would have been shown to a limited, largely sophisticated audience in the capital.

"We don't want to affect our good relations with East Timor and we believe it is important to guard the success of the peace process in Aceh," she said. "TW have to protect the public."

Lalu Roisamri, festival programme director, said the three Timor films – Passabe, Timor Loro Sae and Tales of Crocodiles – were banned last year but the censors said they might be given the green light this year if accompanied by a discussion on the context. "We proposed exactly this but were told the situation was still not suitable," he said.

"The censors are worried that whenever there are problems in East Timor, even when they are internal, Indonesians are accused of orchestrating them." The Aceh film, Black Road, is about the rebellion as seen from GAM's perspective.

Mr Lalu said the censorship board did not reflect Jakarta's maturing society. "Most of the people are conservative, from the military, police and religious figures," he said. "Perhaps the wider population is not yet ready for these films, but the JiFFest audience certainly is."

Sidney Jones, of the International Crisis Group think-tank, described the censors' concerns as "troglodyte". "There's no danger to Indonesia of showing these films," she said. "The political harm of hurting freedom of expression is not warranted."

Indonesia's printed media are among the freest in the region, but last month a Jakarta court sentenced a student to 16 weeks' imprisonment for insulting President Susilo Bambang Yudhoyono during a peaceful demonstration.

The eighth annual JiFFest, which runs from December 8-17, will screen 230 films covering themes as diverse as music, human rights, women and the Middle East.