That ruling said the EU banana policy discriminated against Latin American producers and obliged the bloc to bring its policy on banana trades into compliance by January 1999.
The ruling also said the EU discriminated against companies that distributed the bananas, which includes US companies.
"We regret that efforts between the EU and its Latin American trading partners to negotiate a solution to the banana issue have not been successful," Schwab said in a statement.
"We share the concern of Ecuador and several other Latin American banana exporters regarding the continued existence of a discriminatory tariff rate quota in the EU's current banana regime.
We are hopeful that this formal step will facilitate the removal of that discrimination."
Schwab noted a similar request for the establishment of a panel was submitted by Ecuador on February 23, and in response a WTO compliance panel was set up on June 15.
Colombia also filed a complaint in March.
Former colonies favoured
The WTO had already authorised Ecuador and the US to take action against the EU for its failure to implement the 1996 rulings.
The US ended that action after the EU said it would shift to a tariff-only regime for bananas no later than January 1, 2006, Schwab said.
Despite those commitments, the EU banana policy features a zero-duty tariff rate quota that is allocated exclusively to bananas from African, Caribbean and Pacific (ACP) countries, she said.
ACP countries, many of them former European colonies, benefit from more favorable terms of access to EU consumer markets.
By contrast, bananas from Latin America, where four-fifths of bananas imported by the EU are grown, are subject to a customs duty of 176 euros ($238) per tonne.
The most recent complaint against the EU comes amid heightened tensions in the global trading system, after the collapse earlier this month of an effort by the so-called "G4", the US, EU, Brazil and India, to resuscitate the Doha Round of WTO negotiations.