In February 2000, Defenders of Wildlife and other environmental organizations filed suit against the NOAA Assistant Administrator for Fisheries in the Court of International Trade, alleging that NOAA Fisheries did not lawfully implement the International Dolphin Conservation Program Act, the National Environmental Policy Act (NEPA) and the Administrative Procedure Act. The plaintiffs sought a preliminary injunction from the court to prevent NOAA Fisheries from making "affirmative findings" to lift embargoes against Mexico or other ETP tuna fishing nations. The motion was denied on in April 2000 and the case proceeded to a full hearing.

On 7 December 2001, the Court of International Trade denied plaintiffs' motion for summary judgment and dismissed the lawsuit against NOAA Fisheries. The Court agreed with NOAA Fisheries' interpretation of the IDCPA and upheld the legality of the January 2000 Interim Final Rule in regard to several very specific allegations. The Court also affirmed that the Federal government complied with the NEPA in promulgating the Interim Final rule and in negotiating the 1999 Agreement on the International Dolphin Conservation Program. Finally, the Court held that NOAA Fisheries' "affirmative finding" for Mexico was not arbitrary and capricious. The affirmative finding allows Mexico to export to the United States yellowfin tuna harvested in the ETP using purse-seine vessels with a carrying capacity equal to or greater than 400 short tons.