Brereton was a member of the Opposition Shadow Ministry 1996–2001 serving as Shadow Minister for Foreign Affairs. Assisted by his adviser, Dr Philip Dorling, Brereton was instrumental in revising Federal Labor policy to support self-determination and independence for East Timor. Brereton was a vocal critic of Howard, who supported East Timor's continued integration in Indonesia. He was also strongly critical of the performance of past Labor Governments, in particular Prime Minister Gough Whitlam who acquiesced to Indonesia's intentions to invade East Timor in 1975.