Mr Brough is concerned that some convicted criminals are escaping long jail sentences, and re-offending when they are released from prison.
The 1991 Royal Commission into Aboriginal deaths in custody recommended indigenous offenders only be jailed as a last resort.
But Mr Brough says this means victims of crime are being unintentionally denied justice.
He says fears that Aboriginal offenders may die in custody should not override the need to impose effective punishments.
Violence in Indigenous communities is expected to be discussed at next month's Council of Australian Governments meeting.