Indonesia said in a statement the EU duties on biodiesel were inconsistent with the WTO's Anti-Dumping Agreement and disputed the calculations that they were based on.
"We are ready to file the suit at the first meeting in March 29-30 at WTO headquarter in Geneva," Indonesia's Director of Trade Security Pradnyawati said.
In November 2013, the EU set duties of 8.8 percent to 20.5 percent for Indonesian producers and between 22 percent and 25.7 percent for Argentine producers, to apply for five years in both cases.
The EU argued that by imposing duty on the raw product, soybeans in the case of Argentina and palm oil for Indonesia, they gave an advantage to domestic producers, which allowed them then to "dump" product at unfairly low prices.
Argentina and Indonesia, major exporters of biodiesel, have called the EU measures protectionist.
Both have previously brought complaints before the WTO, with Argentina securing rulings in favour of several of its claims.
The cases have also brought legal challenges, with the General Court of the European Union, the lower of the two EU courts.
Indonesia said the EU duties had caused sales of biodiesel to slump from $625 million in 2013 to an expected $9 million in 2017, according to Trade Map data. (Reporting by Agustinus Beo da Costa; Writing by Ed Davies; Editing by Paul Tait)