The federal government has successfully blocked the release of secret archives that would reveal Australian knowledge of Indonesian war crimes in East Timor, arguing that relations with Jakarta are presently too strained to cope with the potential embarrassment for both countries.

Administrative Appeals Tribunal President Justice Duncan Kerr yesterday said that the National Archives was right to deny University of NSW Associate Professor Clinton Fernandes access to Australian diplomatic papers and intelligence on Indonesian military operations in East Timor from more than 32 years ago.

Attorney-General Senator George Brandis prevented disclosure of the government's reasons for the secrecy in January. Credit:Andrew Meares

A former Australian military intelligence officer turned academic, Dr Fernandes has been engaged in a six-year bureaucratic and legal struggle to secure declassification of records relating to Indonesia's invasion and occupation of East Timor.

On advice from the Department of Foreign Affairs and Trade and Australia’s peak intelligence agency, the Office of National Assessments, the National Archives denied Dr Fernandes access to parts of two Foreign Affairs and Trade files that contain reports about a major Indonesian military offensive across East Timor in late 1981 and early 1982.