Sydney – Two former Indonesian presidents expressed reservations about Canberra-Jakarta relations Sunday, as Indonesia's former intelligence chief revealed his spies had tapped Australian politicians' telephone conversations during the East Timor crisis in 1999.

Abdullah Hendropriyono said Indonesia also bugged the Australian embassy in Jakarta and unsuccessfully tried to infiltrate the Australian Secret Intelligence Service.

Hendropriyono, who resigned as head of intelligence agency Badan Intelijen Negara (BIN) last month, said Indonesian spying activities against Australia had ceased since the two countries joined forces to fight terrorism.

He said the surveillance activity was at its most intensive during the East Timor crisis, when Australia spearheaded an international peacekeeping force to curb Jakarta-backed militias following the former Indonesian province's vote for independence. "In the Timor case, [the targets were] military and both civilian as well," Hendropriyono told Channel Nine.

Former president Abdurrahman Wahid told the television station there was growing resentment at Australia's expanded security presence in Indonesia and he felt that Canberra "meddles in our affairs".

Wahid suggested the September 9 bomb attack outside Australia's embassy in Jakarta that killed nine people was the direct result of perceived interference by Canberra in Indonesian affairs.

Megawati Sukarnoputri, recently ousted as president in national elections, said there had never been an easy relationship between the countries. "It was my experience as president that there was a lack of harmony in the relationship between Australia and Indonesia," she told Channel Nine.

Prime Minister John Howard refused to comment on the spy claims but denied there were strains in the relationship with Indonesia. "I neither confirm nor deny stories about those sorts of security things," Howard told the television station. "Australian democracy is safe and sound and our policy on East Timor was 100 percent correct."

Asked if he would tell the MPs who were supposedly bugged by the Indonesians, Howard replied: "I am not going to talk about any aspect about something like that. "Our relations with Indonesia remain very strong."

Howard said when he became prime minister eight years ago Australia's foreign policy was too heavily skewed towards engaging with Asia and he believed it was now more balanced.

"Now I haven't reduced the Asian emphasis, if anything I've increased it further," he said. "But at the same time I've increased very much the importance of our links with both the United States and Europe, and I think that's rightly so because we're not a country that should put all our eggs in one regional basket – that would be a huge mistake."