The WTO said that Indonesia had made a formal request for consultations with Australia on the issue, which under the Geneva-based organisation's rules is the first step towards a full-blown trade dispute.
Indonesia is the fifth country to challenge Australia at the WTO over its pioneering legislation, passed in 2011 and in force since last December, and which aims to curb smoking by requiring tobacco products to be sold in drab green boxes with the same typeface and graphic images of diseased smokers.
The other cases have been brought by Ukraine, Honduras, the Dominican Republic and Cuba.
The latter trio, all cigar-producers, have cited concerns that the legislation covers all tobacco products, not just cigarettes.
The plaintiff countries maintain that Australia's law breaches international trade rules and intellectual property rights to brands -- arguments rejected by Canberra and which also failed to convince Australia's High Court in a case brought by tobacco firms.
The Geneva-based WTO oversees its 159 member economies' respect for the rules of global commerce. Its dispute settlement process, steered by independent trade and legal experts, can last for years.
In the event that the plaintiffs won their case, the WTO's disputes settlement body would have the power to authorise retaliatory trade measures against Australia if the country failed to fall into line.