CNN  — 

The Navy announced Wednesday that it is launching a broader inquiry into the circumstances surrounding the coronavirus outbreak aboard the USS Theodore Roosevelt aircraft carrier, effectively delaying its recommendation that the ship’s commanding officer be reinstated.

The announcement comes after Secretary of Defense Mark Esper previously declined to immediately endorse the Navy’s original investigation into the issue which included a recommendation to reinstate Capt. Brett Crozier.

“After carefully reviewing the preliminary inquiry into the events surrounding the COVID-19 outbreak aboard USS Theodore Roosevelt (CVN 71), the Chief of Naval Operations, Adm. Mike Gilday, provided me with his recommendations. Following our discussion, I have unanswered questions that the preliminary inquiry has identified and that can only be answered by a deeper review,” acting Navy Secretary James E. McPherson said in a statement.

“Therefore, I am directing Adm. Gilday to conduct a follow-on command investigation. This investigation will build on the good work of the initial inquiry to provide a more fulsome understanding of the sequence of events, actions, and decisions of the chain of command surrounding the COVID-19 outbreak aboard USS Theodore Roosevelt,” he added.

Earlier Wednesday, two US defense officials and an official briefed on the matter told CNN that the announcement was expected.

The new investigation is expected to be led by the Vice Chief of Naval Operations Adm. Robert Burke who will have until May 27 to complete it, according to a Navy official. Burke will have the opportunity to ask for an extension if needed.

Once complete the results of the investigation will be shared with the Chief of Naval Operations Adm. Mike Gilday. If he signs off it will be sent to the acting Navy Secretary to be presented to Esper.

Esper so far has not acted on the Navy’s initial recommendation to restore Crozier to that position despite saying previously that he has “an open mind” on whether the Navy should reinstate the fired commanding officer. And Wednesday’s announcement of a broader investigation into the outbreak aboard the Roosevelt has only added to the uncertainty surrounding Crozier’s future.

President Donald Trump would not say Wednesday whether he’d like to see Crozier return to his job.

“I don’t know him. I think he’s a very, very good man who had a very bad day, and then he wanted to be Ernest Hemingway. He starts writing long memos –you can’t do that when you’re the captain of a ship,” the President said when asked if he’d like to see Crozier return to his post.

“With that being said, as I said, he had a bad day. We all have bad days,” he added.

Rep. Adam Smith, Democratic chairman of the House Armed Services Committee, issued a forceful statement calling on Pentagon leaders to reinstate Crozier, making clear he believed there was “no substantive reason” to remove the Navy captain.

“It is the job of our leaders at the Pentagon to support our national security, not suck up to the President. Yes, these individuals serve at the pleasure of the President, and they must be mindful of that, but in this Administration it appears you must become a sycophant in order to keep your job,” the Washington Democrat said.

“The President’s need for his subordinates to constantly inflate his ego undermines competence throughout this administration. I do not want the Department of Defense to lose competence and simply become another organization whose job it is to pump up the President’s ego,” Smith added.

Meanwhile, sailors from the Roosevelt began returning to the aircraft carrier Wednesday for the first time since they were moved ashore because of Covid-19, the Navy announced in a statement.

As of Tuesday, the ship had 940 active coronavirus cases, compared with 955 on Monday, reflecting an increase in the number of sailors who have recovered.

The handing of the outbreak aboard the aircraft carrier which led to the firing of Crozier, the ship’s commanding officer, and the resignation of the acting Navy Secretary, has been the subject of an initial Navy investigation.

US officials told CNN that senior Navy officials had recommended Friday that Crozier be reinstated but Esper was not prepared to immediately endorse that recommendation.

Two defense officials told CNN that the Navy had expected Esper to endorse the recommendation last Friday.

A Pentagon spokesman said Friday that Esper “intends to thoroughly review the report and will meet again with Navy leadership to discuss next steps.”

Crozier was fired earlier this month for what the then-acting Navy Secretary Thomas Modly said was poor judgment by too widely disseminating a warning among Navy officials about the spread of the virus aboard his vessel, a warning that eventually made its way into the press.

While Modly publicly accused Crozier of sending his letter of warning to 20 to 30 people, the email to which the letter was attached shows that Crozier sent it to 10 people including his direct superior, according to a copy of the email obtained by The Washington Post.

“I believe if there is ever a time to ask for help it is now regardless of the impact on my career,” Crozier wrote in his email, the contents of which a US official directly familiar with the message confirmed to CNN.

Modly resigned days later over his handling of the incident, actions which included a $240,000 trip to Guam where he slammed Crozier and admonished sailors for giving Crozier a rousing send off in public remarks to the crew.

Following his ouster Crozier was initially reassigned to the headquarters of the Naval Air Forces Pacific command in San Diego but has remained in Guam where he is completing a mandatory quarantine period.

After he was fired Crozier was replaced as commanding officer of the aircraft carrier by the ship’s former captain, Rear Admiral select Carlos Sardiello.

The Roosevelt is not the only ship facing an outbreak of the virus. A senior Navy official told CNN last week that there were currently coronavirus cases on 26 US Navy warships, and another 14 had been hit by the virus but the crew members impacted have recovered.

The USS Kidd, a Navy destroyer, has been hit particularly hard.

The number of coronavirus cases among the USS Kidd’s crew has reached 78, nearly 25 percent of the ship’s complement, two Navy officials told CNN Wednesday. The ship is now in port in San Diego and sailors are in the process of being isolated and quarantined on base.

This story has been updated with a statement from the Navy and additional background.

CNN’s Maegan Vazquez contributed to this report.