The official trade level talks, described as friendly and highly constructive, went ahead despite the last-minute withdrawal of Indonesian President Joko Widodo, who was scheduled to make a state visit to Canberra this week for discussions with Prime Minister Malcolm Turnbull and his ministers.

The President, universally referred to in Indonesia as Jokowi, decided to stay home to respond to extraordinary unrest on the streets of Jakarta over the alleged offence caused to the Koran, by the city's Christian and ethnically Chinese governor Basuki Tjahaja Purnama also known as Ahok.

Protesters clashed with police and burnt several vehicles over the weekend, bringing central Jakarta to a standstill with Muslim hardliners insisting the local politician be jailed for blasphemy without a trial.

Jokowi has assured them that the charge against the governor will be dealt with quickly.

Australian officials are keeping a watching brief on the upwelling but at this stage, believe it is a purely domestic matter and not one which will affect two-way business relationships in the immediate term.

Trade Minister Steve Ciobo met with his counterpart Enggartiasto Lukita, with both men keen to advance free trade talks and to build an economic interdependence that, to date, is regarded on both sides as "underdone".

He said the proposed Indonesia-Australia Comprehensive Economic Partnership Agreement reflected the importance of this agreement to both governments and could "transform" the economic partnership.

"Negotiations, re-launched earlier this year, are progressing well as we work towards concluding by the end of 2017. Minister Lukita and I have agreed to pursue an ambitious and high-quality agreement," he said.

Mr Ciobo also noted as a sign of growing trust as memories of the live export ban imposed under the Gillard government fade, that Minister Lukita "indicated that there would be no quotas and that he was in favour of annual permits".

"That will help give industry more certainty and that should also help Indonesia to achieve better beef prices," he said.

Australian exporters have long cited Indonesia's quarterly import permits system for live cattle as a bugbear in which bureaucratic hold-ups over such paperwork could result in Australian ships being held at port for days on end, incurring pierage costs in excess of $25,000 a day and $5 per head of cattle.