Vice Adm. Phillip G. Sawyer, a deputy chief of naval operations and a former commander of the Seventh Fleet in Japan, told The Times that the Navy was following guidance from the Centers for Disease Control and Protection on handwashing, face coverings and other preventive measures, as well as adding additional procedures to limit the potential for the coronavirus to enter its ships, submarines and aircrews. “We learn more everyday,” Sawyer said. “We will continue to evolve our measures to conform to the best practices that we know. We have to be able to protect our force, and we have to be able to conduct the missions that the nation requires of us.”

The Navy is still contending with a major cluster of coronavirus infections aboard the U.S.S. Theodore Roosevelt, the aircraft carrier that has been moored in Guam since late March after an outbreak of the virus while it was at sea. As of Wednesday, a total of 777 sailors from the carrier had tested positive for the virus. A Navy spokesman said that 120 of those sailors had tested positive after leaving quarantine, which led military leaders to re-evaluate the criteria they used for quarantining those suspected of coming in contact with an infected person and for sequestering sailors preparing to deploy.

It is unclear whether the public will be informed of any outbreak of the coronavirus aboard the Ronald Reagan, or any of the Navy’s other ships, while it is at sea. On March 30, the Pentagon announced that it would not make public any information about coronavirus outbreaks in specific units, but in practice it has continued to provide data about cases aboard the Theodore Roosevelt and the hospital ship U.S.N.S. Comfort, which is docked in New York City. According to the documents obtained by The Times, the Navy’s Pacific Fleet commander in Hawaii declared that all information about coronavirus cases aboard Navy ships, aircraft and submarines was now classified at the “confidential” level. A Navy spokesman would not confirm that specific classification directive, but said that sick crew members were allowed to tell their families if they had contracted the virus.

Two Navy officials who were not authorized to speak to The Times raised concerns about how the Ronald Reagan’s commanders would handle the exceptional levels of stress being put on the nearly 5,000-person crew by confining everyone to the ship for up to eight months. A Navy spokesman said that the ship would depart with three chaplains, a clinical psychologist and a counselor, but that it still did not have an assistant for the clinical psychologist on board. The spokesman did not elaborate on specific measures that the ship’s commanders planned to take to keep up morale, but Adm. Michael M. Gilday, the service’s top officer, gave a statement to The Times addressing the issue. “Our sailors and their families are resilient,” he said. “I know they will set an example for their friends, their neighbors and in their local communities on how to make personal sacrifices in the service of the collective good.”

The Navy officials also raised concerns that the indefinite extension of the two-week sequester period already in effect for all aircrew members would further harm the aircrews’ ability to safely fly planes and helicopters, especially after some of the crews’ predeployment training on Guam was cut short last month. The aircrews typically need to fly at least once every two weeks to stay current in their qualifications, but they require even more flight time in the critical run-up to deployment, when they practice landing on an aircraft carrier at sea.