Sydney – The killing of five journalists in East Timor in 1975 returned to haunt Indonesia and Australia Wednesday as an inquest into their deaths drew to a close with a call for war crimes charges to be laid.

At the heart of the case is whether both governments covered up the fact that the so-called "Balibo Five" were deliberately murdered by Indonesian troops ahead of the 1975 invasion of the then-Portuguese territory.

The official line has always been that British, Australian and New Zealand journalists working for Australian television stations died in crossfire in a skirmish in the border town of Balibo on October 16 of that year.

But on Wednesday a top government lawyer said in his summing up of the evidence presented at the inquest over the past four months that it was clear the journalists had been killed in cold blood by Indonesian troops.

"The journalists were not killed by being caught in crossfire... but rather were deliberately killed by the Indonesian troops who had arrived at the Balibo town square," said lawyer Mark Tedeschi.

The journalists had been attempting to surrender to the troops, who were headed by Captain Mohammad Yunus Yosfiah, he said.

"At least three of the journalists were shot by Indonesian troops after an order was given by Captain Yunus Yosfiah. He also joined in the shooting of those three," Tedeschi said.

Another journalist was shot separately and the fifth was stabbed to death by Indonesian officer Christoforus Da Silva, he said. Tedeschi argued that such drastic action would only have been taken with the sanction of officers superior to those on the ground at Balibo.

He said the killing of the journalists could constitute a war crime under the Geneva Conventions and those allegedly responsible could be prosecuted in Australia.

The dramatic call came after officials in both countries had been made uncomfortable by the persistence of coroner Dorelle Pinch's pursuit of the truth on behalf of the family of one of the dead men, TV cameraman Brian Peters.

On Tuesday, Jakarta Governor Sutiyoso cut short an official visit to Sydney after police confronted him in his hotel room and asked him to testify at the inquest about his role as an Indonesian army officer in East Timor in 1975. He refused, flew home and on Wednesday demanded an apology.

Coroner Pinch said later she had merely seized a small "window of opportunity" when she issued a personal invitation to the governor to appear at the inquest.

Earlier this month, she summoned former Australian prime minister Gough Whitlam to her Glebe Coroners Court after hearing evidence that the government had advance warning of the Indonesian attack on Balibo.

The 90-year-old, who was in office from 1972-75, denied that he had seen such a warning and also said he never saw cables suggesting the journalists had been executed by the Indonesian military.

The strain the inquest has put on relations between Australia and Indonesia was further illustrated Wednesday in a dispute over whether Jakarta had been told not to worry about the hearing.

Indonesia's Foreign Minister Hassan Wirajuda said Canberra had basically guaranteed his government there would be no fallout from the inquest, the Australian Broadcasting Corporation reported.

His Australian counterpart Alexander Downer, however, told the national broadcaster that was not the case.

"I wouldn't put it in those terms, we had a very brief discussion about this quite some time ago," he said. When pressed, Downer denied he had offered any such assurance.

Peters and fellow Briton Malcolm Rennie were working for Australia's Channel Nine when they were killed, while Australians Greg Shackleton and Tony Stewart, and New Zealander Gary Cunningham, were working for Channel Seven.