Foreign Minister Julie Bishop told Fairfax Media on Thursday that Australia did not "believe that the conclusion of permanent boundaries between Australia and Timor-Leste requires Australia to renegotiate boundaries with Indonesia".

"We have a settled understanding of boundaries with Indonesia which has served both countries well for several decades," she said.

"During the conciliation with Timor-Leste, we have kept the interests of Indonesia in mind and have briefed Indonesia on the terms of the treaty between Australia and Timor-Leste."

The Foreign Minister's comments come a day after Indonesia's director-general of legal affairs and international treaties, Damos Agusman, told Fairfax Media "the Perth treaty cannot enter into force as it stands now as it, inter alia, covers area that now belongs to TL [East Timor], and the object of the conciliation".

Mr Agusman's comments will likely ruffle feathers in Canberra as will the suggestion from Jakarta that it "reserves all its rights against any outcomes that might potentially affect" its sovereign rights.

The Perth treaty was agreed in 1997 between Australia and Indonesia – though it has not yet been ratified – and sets most of the maritime boundary of the two nations at the so-called median point between the two countries.

This has meant Indonesia's fishing rights extend further south than its right to explore the seabed for oil and gas, which is governed by an earlier treaty from 1972. That treaty sets the boundary between the countries much closer to Indonesia.

Also on Thursday, a spokesman for Indonesia's Foreign Ministry confirmed President Joko Widodo would have a half-hour bilateral meeting with Prime Minister Malcolm Turnbull at the ASEAN-Australia summit in Sydney, followed by dinner at the Prime Minister's residence.

The two nation's will not finalise a much-delayed free trade agreement at the summit, as had been hoped, but the official said Jakarta still hopes to finalise it by the end of the year.

Nations attending the summit are also expected to sign a memorandum of understanding on counter-terrorism that covers issues such as greater intelligence sharing and cross-border movements.

International law expert Professor Donald Rothwell has warned renegotiating a complex agreement such as the Perth treaty could potentially make diplomats in Canberra very nervous.

Mr Agusman's comments came after an historic agreement between East Timor and Australia was struck in New York over maritime boundaries, which will potentially see billions in extra revenue flow to East Timor from the Sunrise gas field, assuming development can now take place.