The footage, broadcast on ABC, showed cattle being flogged and taking minutes to die after their necks were slashed.
Some MPs have called for a total ban on the trade with Indonesia, worth more than A$300m (£200m; $320m) a year.
But Indonesian officials have asked Australia not to rush into a decision.
The head of animal welfare at Indonesia's agriculture ministry, Sri Mukartini, said: "Animal welfare is a relatively new issue in Indonesia. We're still developing regulations."'Systemic problem'