The corps, the agency in charge of the project, did relocate 924 other, nonendangered corals.

Florida and the Caribbean are rapidly losing their coral reefs, some of the most diverse ecosystems in the world, and the damage has raised intense criticism of how the Army Corps of Engineers has managed the project.

Environmentalists sued the corps in October, saying it violated the Endangered Species Act and the terms of a permit issued by the State Department of Environmental Protection.

“We’ve seen profound and severe impacts to our reef just off of Miami; it looks like a moonscape,” said Rachel Silverstein, the executive director of Biscayne Bay Waterkeeper, the lead environmental group bringing the lawsuit. “This damage stems from the fact that the corps and the contractors simply weren’t following the rules that were laid out for them when they started this project.”

Reefs around the world have experienced drastic declines as a result of pollution, acidification and overfishing. Higher ocean temperatures, which can bleach coral and kill it, have also damaged reefs. Some coral near the port suffered from bleaching last summer. In certain areas of South Florida, 90 percent of the coral is gone.

In Florida, coral reefs lure residents and tourists, who dive and snorkel to see their vivid colors and the tropical fish that they attract. Just as important, reefs serve as crucial wave buffers during tropical storms, protecting beaches and shoreline homes.