The complaint by Robin des Bois accuses the company, Maersk, and the crew of the Svenborg Maersk of "unacceptable light-mindedness," Radio France International reported Friday.
The 20-foot and 40-foot shipping containers fell off the ship this month off the coast of France during a storm with 30-foot waves and 60-knot winds, CNN reported.
The containers were found missing when the ship docked in the Spanish port of Malaga for repairs.
Maersk initially reported 70 containers were lost; on Wednesday, it upgraded the total to 517.
The environmental group called the lost containers "a permanent danger for fishermen, coastal communities and the environment." It said Maersk was guilty of pollution and "abandoning waste."
The company said 85 percent of the containers were empty. The rest contained dry goods; none carried hazardous materials.
By Friday, 13 containers had been recovered.
Palle Laursen, Maersk's vice president of operations, told CNN the company was reviewing its policies "to avoid similar incidents in the future."
How many shipping containers are lost annually is unclear, CNN said. In 2011, the World Shipping Council estimated the number at about 675. A shipping insurer, the Through Transport Club, says fewer than 2,000 containers are lost each year, while CNN notes other industry sources say annual losses may be as high as 10,000.