Indonesia says the case of the Balibo Five is closed and insists an Australian coroner's claim its soldiers may have committed war crimes won't damage relations between the countries.

Deputy NSW Coroner Dorelle Pinch on Friday found Indonesian soldiers deliberately killed five Australian-based journalists in October 1975 to stop them reporting on Indonesia's invasion of East Timor. She says war crimes may have been committed and will refer the matter to Australia's attorney-general.

Indonesia has always insisted the Balibo Five were killed in crossfire in the border town of Balibo during its invasion of East Timor.

In Jakarta, Indonesian foreign ministry spokesman Kristiarto Legowo said the coroner's finding would do nothing to change its position.

"It will not change Indonesia's stance that for us it is a closed case and we are still in the position that they were killed because of crossfire between conflicting sides at the time. Whatever the coroner's recommendation, it will not change Indonesia's position on that."

A spokesman for Indonesian President Susilo Bambang Yudhoyono also said the case was "closed" and was confident the coroner's findings would not damage relations between Canberra and Jakarta.

"Our relationship is very strong," Dino Patti Djalal told AAP. "It is endurable to withstand any issue. So I don't think this news will rock our boat. It's a pity what happened to them but we've moved on."

However an Indonesian military spokesman, Air Vice Marshal Sagom Tamboen, suggested relations could be damaged by the issue. "I can see that this thing could worsen relations between Indonesia and Australia," he said.

Air Vice Marshal Tamboen rejected the coroner's findings. "If they concluded that the TNI (the Indonesian military) seemed to arrange it (the deaths), where did they get their sources? It's a premature conclusion."

Air Vice Marshal Tamboen said the report of the coroner, who tried and failed to have key former Indonesian officers give evidence at the inquest, was one-sided. "They never asked us. And the matter is already closed. What is their new evidence?"

The military spokesman questioned whether the NSW coroner was able to brand the killings a war crime. "Is that what international conventions say? Are they a competent body to say that?"

The Indonesian embassy in Canberra would not comment on the findings.

Ms Pinch said the Balibo Five had been killed on the orders of Indonesian special forces officers including Yunus Yosfiah, later to become a minister for information.

Contacted in Jakarta, the now retired Yosfiah refused to comment. "I've talked about that many many times," he said, before hanging up.

Yosfiah, who refused repeated requests to give evidence to the NSW inquest, has denied ordering or taking part in the killings.

The inquest ruling comes days after Indonesia's parliament agreed to ratify a key security treaty between the two nations, known as the Lombok Treaty.

The signing of the treaty a year ago was a key step in a thawing of relations between the two nations, after Indonesia's ambassador to Australia was recalled amid a row in 2006 when Australia granted protection to 43 Papuan asylum seekers.

Indonesian human rights group Kontras welcomed the Balibo finding, but feared any action would be limited by the two nations in order to maintain their good relationship.

Kontras coordinator Usman Hamid said Indonesia had shown reluctance to assist in the case. However, he said Indonesia needed to learn lessons from its past mistakes, such as the Balibo Five killings, in order to build a stronger democracy.

"In terms of human rights awareness this case is very important to deliver the message about the universality of human rights," Hamid said. "Of course its not easy for us to convince Indonesian authorities to bring those responsible to justice."

Much would depend on how the Indonesian and Australian governments approached the case.

"If you look at the case of Papua or the Lombok pact, these two examples show how both governments are still putting the issue of human rights as internal affairs," Hamid said.

"The Lombok pact seems to be a way that both governments are trying to not interfere in each other's domestic affairs. "But for us, human rights abuses are not domestic issues. Australia and Indonesia have obligations under international law."

Hamid said if Indonesia continued to resist legal efforts at justice over East Timor abuses, it could undermine its current role in the United National Human Rights Council and as a non-permanent member of the UN Security Council.

"In spite of the limited result in the future of the justice process, I think it's really important to send a message to Indonesia, to the world, that an Australian court has condemned war crimes, wherever they are committed."

The Balibo Five case caused tension between the two nations in May, when the then Jakarta Governor Sutiyoso angrily cut short a Sydney visit, after being invited to testify at the inquest.