Navy Capt. Brett Crozier, who was relieved of his command of the aircraft carrier Theodore Roosevelt after taking actions to protect his crew from a shipboard outbreak of coronavirus, appears close to being returned to his post.

In what experts saw as a surprising move, Navy leaders have reportedly recommended that Crozier be reinstated as commanding officer of the Roosevelt, congressional sources told The Chronicle on Friday.

Top Navy officials have briefed Defense Secretary Mark Esper about the report, which largely cleared the 50-year-old Santa Rosa native, the sources said. Esper has indicated that he will likely follow the Navy report’s findings, but has asked for more time to weigh Crozier’s reinstatement, the sources said. The New York Times was the first to report the Navy recommendations Friday.

The recommendation came from Chief of Naval Operations Adm. Michael Gilday and Acting Navy Secretary James McPherson. Gilday first met with Gen. Mark Milley, chairman of the Joint Chiefs of Staff, on Tuesday to explain his recommendation.

It was not clear when Esper might act. Jonathan Hoffman, assistant to the secretary of defense, confirmed the Friday meeting to The Chronicle, but said Esper had more to mull following the briefing.

“After the secretary receives a written copy of the completed inquiry, he intends to thoroughly review the report and will meet again with Navy leadership to discuss next steps,” Hoffman said.

Lawrence Korb, a former assistant secretary of defense in the Reagan administration, said Friday that it was “highly unusual” for the Navy to reinstate a captain in this manner.

“The Navy is recognizing that Capt. Crozier was concerned about the people on his ship,” Korb said. “And he was right. This was a serious thing. One person has died.”

The announcement comes three weeks after The Chronicle first published the news about Crozier’s stark warning to Navy officials that sailors on the Roosevelt could die if there wasn’t a quick evacuation of the ship. A letter from Crozier, which became public after he shared it with several other officers, sent shock waves through the Navy. Many observers described Crozier’s action as courageous but also a likely end to his promising career.

In his letter, Crozier described a deteriorating scene on the carrier since it had docked in Guam on March 27. He pleaded for resources to properly quarantine 90% of his crew away from the crowded confines of the ship.

“This will require a political solution but it is the right thing to do,” Crozier wrote. “We are not at war. Sailors do not need to die. If we do not act now, we are failing to properly take care of our most trusted asset — our Sailors.”

Soon after his warnings became public, Guam opened hotel rooms for his sailors, and an evacuation of much of the crew began.

But Crozier was relieved of his command, with Navy leaders saying his wide sharing of his memo broke the chain of command and undermined national security. He left his ship to a hero’s departure, his crew chanting his name. A day later, former Acting Navy Secretary Thomas Modly berated Crozier in a speech to his crew and said he betrayed the Navy. Modly resigned less than 24 hours later.

Korb, a retired Navy captain who is now a senior fellow at the left-leaning Center for American Progress think tank, said that what can be learned from Crozier’s story “is that we ought to respect those who speak out when they see something that isn’t going the way it should, whether it is on a battleship or the military battlefield.”

Other military experts were equally surprised.

“This is unprecedented,” said Mark Cancian, a senior adviser with the Center for Strategic and International Studies think tank in Washington, D.C., and a Marine colonel who served for 37 years before retiring.

“From all I can see, Admiral Gilday CNO has made a good call,” retired Adm. James Stavridis, former NATO Supreme Allied Commander Europe, told The Chronicle Friday in an email, adding that “we will know more when (the) investigation is released.”

The concerns Crozier expressed in his letter appear to have been validated. As of Friday, 856 Roosevelt sailors had tested positive for the coronavirus. And as the captain had requested, most of the ship’s crew — more than 4,200 sailors — has been moved ashore, many into hotel rooms. One sailor has died, another has spent time in intensive care and four remain hospitalized.

The report recommendation comes less than a week before the Navy plans to begin bringing sailors back aboard the Roosevelt, The Chronicle has learned. By Thursday, the Navy plans to send 700 healthy sailors back on board to replace a skeleton crew that has worked there during the ship’s evacuation and quarantine plan, a sailor told The Chronicle.

Sailors who have been isolating in Guam hotels for more than two weeks must test negative twice in screenings taken 48 hours apart. The final tests will be done Saturday in Guam, and sailors will wait for the results from a South Korean lab before being allowed back onto the Roosevelt, the sailor said. The Chronicle agreed to withhold the name of the sailor, who was not authorized to speak to the media, in accordance with its anonymous sources policy.

The plan to repopulate the Roosevelt comes as the Navy finds itself with a new coronavirus battle on the destroyer Kidd. On Friday, the Navy announced 18 sailors on the ship have tested positive. The first sailor to test positive was flown off Thursday and returned to the United States. The sailor is stable and receiving care in a San Antonio hospital.

The Navy sent a medical team to the ship to conduct tracing and on-site testing, and by Friday morning, 17 more sailors had tested positive. The Navy said it expected “additional cases.”

“The first patient transported is already improving and will self-isolate. We are taking every precaution to ensure we identify, isolate, and prevent any further spread onboard the ship,” said Rear Adm. Don Gabrielson, commander of the U.S. Naval Forces Southern Command, in a statement. “Our medical team continues coordinating with the ship and our focus is the safety and well-being of every Sailor.”

The destroyer will return to port, and the crew will clean and disinfect the ship.

The military has been grasping how to combat the coronavirus since the Roosevelt outbreak, especially the Navy, whose sailors are in close quarters aboard ship.

“The Navy has lessons learned ... and they are quickly applying those to this case,” said Hoffman.

As far as bringing sailors back onto the Roosevelt, the sailor told The Chronicle, the crew aboard the warship has been cleaning and disinfecting various areas of the ship and closing those off. On the final day, those sailors will clean up the areas where they have resided and the healthy 700 sailors returning onboard will move into the areas cleaned weeks earlier and slowly repopulate the ship.

Those leaving the ship will start their own 14-day quarantines, taking the carrier’s stay in Guam into at least May.

Hoffman declined to share any details of those plans Friday in a Pentagon briefing.

“This is a learning environment. ... We would rather take a little more time on the front end to get to a place where we have more confidence that the crew is safe and that the virus is no longer on the ship than being in the position a month from now where there’s a second wave,” he said.

San Francisco Chronicle staff writer Tal Kopan contributed to this report.

Matthias Gafni and Joe Garofoli are San Francisco Chronicle staff writers. Email: matthias.gafni@sfchronicle.com, jgarofoli@sfchronicle.com Twitter: @mgafni, @joegarofol