John Kerin and Steve Lewis – A classified document warning intelligence analysts of the risks of providing advice challenging a "pro-Jakarta lobby" in the bureaucracy was circulated within Australia's defence agencies in the late 1990s, a former senior analyst has told The Australian.

The document warned analysts they could risk their careers in providing advice that challenged the alleged lobby over Australia's appeasement of Indonesia and its position on East Timor before its dramatic vote for independence in 1999.

The document warned that there were agents of the Indonesian Government within their midst as well as senior bureaucrats who did not want to hear criticism of Jakarta.

The former analyst's disclosure has been confirmed by at least one other former intelligence officer.

It follows a claim by the intelligence whistleblower Lieutenant-Colonel Lance Collins that a pro-Jakarta lobby in the Defence Intelligence Organisation quashed his 1998 warning of violence by Indonesian-backed militia in the lead up to East Timor's independence.

The new allegation came as the Government continued to resist Lieutenant-Colonel Collins's demand it release publicly all documents relating to his claims of bungling and bias within the DIO.

Lieutenant-Colonel Collins, who on Monday stepped up his demand for a royal commission into the intelligence services, has accused the Howard Government of selectively releasing reports into his case to discredit him.

Opposition parties have supported the call for a royal commission into the intelligence services, but John Howard says it is unnecessary.