Australia's government is fighting to keep proof of Indonesian war crimes from public view, and the effort is apparently meant to keep Indonesia's government happy.

The case shows just how far Australia is willing to go to keep Indonesia onside, especially as immigration policy looms large.

On Wednesday, the Federal Court of Australia sent a case regarding public access to government records that could reveal details of Indonesian war crimes in East Timor during the 1975-1999 occupation back to the Administrative Appeals Tribunal. The Attorney-General's Department and the National Archives are arguing to keep the files under wraps.

At the other end of the fray is Clinton Fernandes, a former Australian military intelligence official turned political studies professor.

"This is about whether the executive branch of government can conduct policy and withhold information without judicial oversight," Fernandes told VICE News during an adjournment in federal court proceedings.

The world has long wondered what exactly happened during Indonesia's almost 25-year occupation of East Timor. Amnesty International estimates that some 200,000 East Timorese — roughly a third of the country's population — were killed or died of sickness and starvation during the occupation.

Indonesia won't be releasing its records from this period any time soon, but its Australian neighbor has diplomatic cables and intelligence reports that can help provide an accurate account of alleged war crimes — and Fernandes is fighting his third case in seven years to access these documents.

"I'm pursuing documents from 1981 when, between August and September, the Indonesian military rounded up 145,000 men — subsistence farmers — and marched them across the island in front of their military as human shields, trying to flush out resistance fighters," he said, speaking of an operation known as the "Fence of Legs" in Indonesia. "During this time, our diplomats received briefings from Indonesian officials. I wanted to know what we knew, so I filed for the documents."

Ordinarily, Australian government documents are available to the public after 20 years, or 30 in the case of cabinet documents, but they can be withheld under special circumstances. These include the material's release posing a threat to national security or foreign relations.

When the National Archives refused Fernandes's request, the government cited the damage the disclosure could do to the relationship with Indonesia as the reason for not releasing the documents. Fernandes responded by petitioning the Administrative Appeals Tribunal.

"Suharto, the dictator at the time, is dead," Fernandes told VICE News. "All the generals are either dead or retired. East Timor, where all of this happened, is independent now. From my point of view, there's no conceivable harm in releasing this information."

"They've said that the documents don't involve signals intelligence in open court, and their argument doesn't relate to jeopardizing the ability of the government to gather intelligence," he added. "This is significant. I'm very conservative when it comes to damaging our intelligence gathering. I don't want to compromise our ability to defend ourselves, but this argument is more like, Indonesia will be angry and sulk."

Attorney-General George Brandis has ordered that arguments be heard under what is known as a "public interest certificate," which prevents Fernandes or his legal team hearing evidence the government puts forward. This has applied to the Administrative Appeals Tribunal hearing, and now the hearings in Federal Court. The government has also obtained a "top secret" classification for the evidence it is presenting.

"It leaves us to basically take a stab in the dark and guess what their case is, so that we construct a case that addresses their evidence," Fernandes said of the cloak of secrecy. "But they can presumably rebut our evidence in closed session."

Such measures are usually reserved for cases involving ongoing threats to national security, and have their critics even then. So why is the Australian government going to such lengths to shield Indonesia's reputation?

The relationship between the two countries has been on thin ice of late, particularly after Edward Snowden's leaks revealed last year that the Australian Signals Directorate had tapped the phones of then-Indonesian President Susilo Bambang Yudhoyono and his wife.

The discovery prompted Indonesia to recall its ambassador from Australia in response, and demonstrators at mass protests in Jakarta burned Australian flags and images of Australian Prime Minister Tony Abbott, who refused to apologize for what he called "reasonable intelligence-gathering activities."

Indonesia also conducted a review of its cooperation with Australia in foreign affairs, and insisted that Australia sign a code of conduct before the relationship was normalized that included promising not to use intelligence gathering in a way that would harm the other party.

But while normal diplomatic relations resumed, they have nevertheless remained somewhat tenuous, so much so that both candidates during Indonesia's presidential election this year acknowledged during televised debates that the relationship was poor.

"I think we are always regarded as a weak country," Joko Widodo, the eventual winner of the presidency, said of the relationship in June. "We have to show that we are a country with dignity, and not let other countries treat us as weaklings," he went on, adding that if disputes could not be resolved over asylum seekers traveling via Indonesia to Australia, then "we can bring them [Australia] to international courts if necessary".

Indonesia's cooperation is crucial to the Australian government's pledge to end the arrival of boatloads of refugees in Australian waters every year. Australia received more than 18,000 refugee access requests between 2012 and 2013. When Abbott took office last year, a central plank of his government's policy platform was to stop the boats, including by forcibly turning them back to Indonesian waters.

During the suspension of diplomacy over the Snowden revelation, Indonesia's navy refused to accept "tow-backs" of refugee-filled boats from the Australian navy, creating political fallout for Abbott's government as it struggled to maintain its border protection policy.

The government appears to be concerned that the East Timor documents case not give its critics in Indonesia ammunition that could force Joko Widodo's hand.

The people of East Timor, meanwhile, are left to watch this calculation of regional diplomacy on the sidelines.

"During the occupation they were living in a subsistence economy, and as it was not a society that had a high level of education, they weren't able to necessarily record what was going on," Fernandes explained. "So for East Timorese I talk to, they're delighted that these records are starting to come out, because for them these records are evidence of the lives their fathers and mothers and grandparents had. It's proof that it happened."