“This Florida reef is as important to our country as the sequoias of California, and we are losing it faster than we can figure out why,” said Rachel Silverstein, the executive director of Miami Waterkeeper, a nonprofit environmental organization that has sued the Army Corps of Engineers over coral damage. “There are a lot of stressors that are impacting and killing coral reefs, but this is a hyper-local example of something we could easily have prevented.”

The agency’s analysis, obtained by The New York Times, contradicts a December report by the corps, which primarily blamed white plague for the coral damage on reef sections near the dredge. In the corps’s report, scientists said that white plague was responsible for 85 percent of the coral deaths in the upper and middle parts of the reef and in the control site, and for 18.3 percent of the deaths of coral closer to shore. The report failed to highlight that 93 percent of the corals closer to the dredge had partially died because of sediment, compared with 7 percent at sites farther away, Ms. Silverstein said.

Scientists for the National Oceanic and Atmospheric Administration disagreed with the corps’s emphasis on white plague disease. Rather, they concluded that the majority of the reef, stretching beyond 3,000 feet, showed conclusive damage to corals by dredging sediment.

The agency’s survey of the extensive damage comes at a time when Fort Lauderdale is seeking final congressional approval for the dredging of its own port, Port Everglades, one of the largest in the country. The dredging project to deepen the port cleared a crucial Senate committee last week as part of a larger water bill and is headed for the Senate floor. Coral reefs are critical to South Florida because they help lessen the damage from hurricanes, are important to marine biodiversity and lure tourists.

Environmentalists have warned Congress and the state that the corps’s plan to lessen the damage to corals in that area is flawed because it does not take into account new information, much of it bolstered by state and county scientists, about the extent of the coral damage from the port of Miami’s dredge. Expansion of Port Everglades is expected to begin next year.