Former prime minister Malcolm Turnbull has arrived in Bali for a global oceans conference — but his bigger task will be to try and mend damaged relations between Australia and Indonesia.

Malcolm Turnbull, who forged a close relationship with the Indoensian president Joko Widodo, was asked by Prime Minister Scott Morrison to represent Australia at the UN conference, a choice was criticised by prominent figures inside the Coalition, including Barnaby Joyce and Tony Abbott.

The visit comes amid concerns Malcolm Turnbull's dumping as Prime Minister has put the free trade agreement with Indonesia at risk.

A subsequent announcement in the lead up to the Wentworth by-election that Australia was considering moving Australia's Israeli embassy to Jerusalem also angered Jakarta.

Malcolm Turnbull has acknowledged relations between Australia and Indonesia will be on the agenda when he meets with Joko Widodo later today.