Air Chief Marshal Angus Houston has defended his support for Jakarta Governor Sutiyoso over a Sydney coroner's bid to question him about the 1975 killings of five newsmen, despite fresh evidence accusing the governor of torture.

Australia's Chief of Defence Force said he was unaware of the torture allegations before they appeared in Saturday's Canberra Times and could not "provide any additional comment" on the matter.

A diplomatic row erupted after Lieutenant-General Sutiyoso abruptly cancelled an official visit to Australia in early June when Acting Coroner Dorelle Pinch sent a detective to his hotel to request his testimony. He claimed police had entered his room using a master key.

Evidence had earlier been tendered identifying General Sutiyoso as a commander of the 1975 Indonesian special forces operation in which five television reporters were killed.

The inquest, which is expected to conclude soon, is into the death of 26-year-old cameraman Brian Peters, one of the so-called Balibo Five, who lived in Sydney.

At a press conference on his return to Jakarta from Sydney, General Sutiyoso angrily denied involvement, and Indonesian protesters converged on the Australian embassy.

Air Chief Marshal Houston said at the time that the governor had told him he was nowhere near Balibo when the killings occurred, an added that he "never doubted his innocence". He described the governor as a "long- standing friend of Australia".

The Canberra Times revealed exclusively on Saturday that Sutiyoso, then an army captain, had run torture sessions for military prisoners in East Timor's second city of Baucau less than two months after the Balibo killings. Witnesses said Captain Sutiyoso helped set up a torture centre in a former Portuguese hotel, although its commander was a Major Leo, also identified by the inquest as a Balibo commander.

Joao da Costa, who was held for three months in 1976 at the torture centre, said, "Sutiyoso often led my interrogations". "I was given electric shocks, and had cigarettes stubbed out in my face and on my body during interrogations commanded by Sutiyoso," he said.

"On one occasion I was covered in blood. I pleaded with him to point his gun at me and give me a bullet." Another Baucau witness known as FS said he saw Captain Sutiyoso at a holding centre at nearby Tiu Lali where prisoners awaited execution.

In response to questions from The Canberra Times, Air Chief Marshal Houston said yesterday that he felt "very deeply for the families who suffered this terrible tragedy".

He said his remarks in June had expressed "regret at the NSW police incident which occurred in the hotel in which Governor Sutiyoso was staying during his visit to Sydney".

NSW premier Morris Iemma, who hosted Governor Sutiyoso's visit to Sydney in June, added his apologies at the time to those of Air Chief Marshal Houston and Australian ambassador to Jakarta Bill Farmer.

Mr Iemma's media adviser said yesterday that the premier stood by his apology. "He apologised to the Governor of Jakarta for the breakdown of communications between NSW government agencies," the spokesman said. He said the torture evidence "wouldn't change the circumstances" under which the apology was offered.