At the beginning of this month's long overdue inquest into the deaths of the five Australian-based newsmen at Balibo in 1975, the Crown counsel heralded the hearings as the first "open, public and completely independent" inquiry of a judicial nature into the case. Yet as the inquest moved this week into the knowledge of Australia's electronic intelligence agency, the Defence Signals Directorate, the court was closed to the public and the media for long stretches of key testimony.

The Deputy State Coroner, Dorelle Pinch, agreed to these conditions after the Federal Government's counsel produced sworn letters by the DSD's chief that Australia's defence would be weakened by disclosure of its "sources and methods" – even those from 1975. To her credit, Ms Pinch has kept some DSD evidence in the public domain, including content of certain intercepted Indonesian military signals. But the interested public will continue to wonder whether the agency is revealing all that it knows.

As noted by counsel for one bereaved family, attempts to find out what happened at Balibo met 30 years of "deceit and cover-up" in Canberra. Already DSD intercepts are appearing that were not produced to earlier, internal government inquiries. Two former senior public servants have recalled in detail seeing, while with the Hope royal commission into intelligence and security in 1977, a critical intercept that seems to have vanished. They see it as entirely possible this has disappeared into some "deniable" DSD oubliette. Questions have been raised whether the DSD tones down some intercepts in translation. The agency is thus under some scrutiny itself.

This will double public scepticism about its claim that the "sources and methods" of 31 years ago remain vital national security secrets. The Soeharto regime fell nearly nine years ago. That the DSD can intercept radio signals and tries to crack foreign ciphers is widely known, not least to Indonesia. The agency and its targets have moved on to an entirely new age of satellites, digital communications and computer-generated ciphers.

The legal precedents cited by the Commonwealth counsel for closed hearings relate to recent or continuing terrorism cases, in which security agencies are battling a present-day threat, not to the vintage electronic intelligence scene of 1975. In this case, the public interest in open justice must outweigh DSD jitters. The coroner should have refused the Commonwealth's application for secrecy, and allowed senior federal judges to decide the issue if it went to appeal.