Australia's "megaphone" diplomacy and lack of consultation with Indonesia over policies like boat turnbacks has caused widespread unhappiness in Jakarta and harmed relations, the head of the peak body representing Australian businesses operating there says.

The unusually blunt assessment came as Indonesia dramatically cut its permits for live cattle exports from Australia for the three months ending September to 50,000 animals, significantly fewer than the 200,000 expected and the 250,000 quota for the quarter just gone.

Agriculture Minister Barnaby Joyce described the decision as "disappointing" and vowed to find alternative markets. Senior government ministers denied the decision was linked to the tense diplomatic relations between the two nations.

However, Debnath Guharoy, president of the Australia Indonesia Business Council, said there was little doubt Australia was unpopular with the Indonesian government at the moment.