Marian Wilkinson, Sydney – An Australian intelligence agency learned from an intercepted Indonesian Army radio message that Australian television crews were in danger and would be targeted, hours before the October 16, 1975, attack at Balibo in East Timor, a new book has revealed.

But the Defence Signals Directorate (DSD) withheld the radio intercept from Canberra apparently to prevent the then prime minister, Mr Gough Whitlam, or his key ministers from trying to intervene to save the journalists. The authors say the DSD did not want to risk alerting the Indonesian military that its secret signals were being routinely broken by Australia.

Five TV newsmen – Greg Shackleton, Gary Cunningham and Tony Stewart of Channel 7, and Malcolm Rennie and Brian Peters of Channel 9 – were deliberately killed several hours later by Indonesian special forces seizing Balibo and other towns on East Timor's border in a covert invasion.

After the attack, the DSD issued a more innocuous translation of the intercepted message to the small high-level circle of politicians, defence and foreign affairs chiefs.

The disturbing disclosures are made in a new book on the deaths of the five newsmen by Australian National University defence expert Professor Desmond Ball and The Sydney Morning Herald's foreign editor, Hamish McDonald, called Death in Balibo, Lies in Canberra.

Also disturbing is the revelation that records of both the original and subsequent translations of the top-secret intercepts are missing from the DSD archives, and from a closely held "Blue Book" of Balibo-related material that has been guarded by a specially appointed custodian within the Defence Intelligence Organisation in Canberra since the late 1970s. The disclosures are certain to bring calls for a judicial inquiry into the Balibo killings.

The authors charge that Canberra's complicity in the Indonesian effort to annexe then Portuguese Timor by force are behind cover-ups that continue today. They also question the apparent unwillingness of Mr Tom Sherman, the Federal Government's special investigator into the newsmen's deaths, to follow leads given to his second inquiry in 1998-99 into the intelligence cover-up.

The authors call for the opening of all Balibo records, arguing that Jakarta was well aware of United States and Australian capabilities at the time, and has since replaced the World War II-era encryption machines it used in 1975 with more secure computerised systems and landlines.

"The Australian-Indonesian relationship has been more damaged by the widespread feeling among the general public that the official relations are enmeshed in lies and deceit," they write. "This can only be rectified by the release to public scrutiny of all official records, including signals intelligence material, relating to the tragedy."

The book details how the Indonesian invading force commanded by Colonel Dading Kalbuadi learned of the presence of Australian and Portuguese TV crews at Balibo by listening to radio messages between Fretilin commanders in East Timor.

Colonel Dading's own messages, to his unit commanders in the field, and back to Jakarta, were in turn monitored by Australian signals stations at Shoal Bay, near Darwin, and at Cabarlah, Queensland, assisted by a DSD radio unit aboard a Navy ship near Timor.

The book quotes members of the intelligence community confirming that several hours (one said five hours) before the attack, DSD picked up and processed an exchange of signals between Colonel Dading in Timor and the then Indonesian chief of military intelligence, Major-General Benny Murdani, supervising the operation for the Balibo attack in Jakarta.

Colonel Dading reminded General Murdani about the presence of foreign journalists at the border and the difficulties this presented, given that his troops were posing as local pro-Indonesian partisans. "We can't have any witnesses," General Murdani is alleged to have said. Colonel Dading is said by the intelligence sources to have replied in words to the effect of: "Don't worry, we already have them under control."

The authors say it is unclear whether the exchange happened five hours before soldiers entered village, at 6am local time, or before the preliminary barrage of artillery and mortar fire which started at 11pm local time the night before.

In the latter case, Canberra would have had about 12 hours to save the newsmen. While getting a message to the newsmen would have been physically difficult (the nearest telephone was about two hours' drive away), the authors argue the Australian Embassy in Jakarta could have been alerted to intervene with Indonesian leaders.

"However, this intercept does not appear to have left DSD headquarters" – then in Melbourne – the book says. "A decision to withhold it was evidently taken at the highest levels of DSD, by officials who were not prepared to take the risk that politicians or other government departments might act on the knowledge in a way that would expose to the Indonesians the extent of Australia's sigint [signals intelligence] capability."

The authors claim the critical decision, "almost certainly involved both the DSD director, Ralph Thompson, and his most senior operations officer, Mos [Mostyn] Williams". Thompson is now dead, and DSD told the second Sherman inquiry it cannot find records of the intercept. However, a DSD staffer at Shoal Bay showed the original translation to staff of the Hope royal commission into security and intelligence in 1977. The two staff confirmed the intercept and its contents to Mr Sherman.

In the event, Mr Whitlam and his ministers were briefed within hours of the attack about intercepts confirming the newsmen's deaths, and that their bodies had been incinerated. But they accepted strong advice from then Defence Department head Sir Arthur Tange that this knowledge be held from the public and bereaved families until confirmed by "open" sources.

[Death in Balibo, Lies in Canberra is published today by Allen & Unwin.]