The Centers for Disease Control and Prevention (CDC) submitted the plan as part of efforts to control the spread of the deadly virus, before White House officials ordered the recommendation to be removed, a federal official with direct knowledge of the plan told the Associated Press news agency.
Trump administration officials have since suggested certain people should consider not travelling over the outbreak, which has killed at least 19 people in the US, but stopped short of the guidance sought by the CDC.
The official was not able to say why the recommendation was removed from the plan and a spokesperson for the US vice president, Mike Pence, denied the story.
“This story is complete fiction. It was never a recommendation to the Task Force,” Katie Miller, Mr Pence’s press secretary, said on Twitter.
On Saturday, Mr Pence gave a similar recommendation to a narrower group – older people with serious health problems – after a meeting with cruise ship industry leaders in Florida.
“If you're a senior citizen with a serious underlying health condition, this would be a good time to practice common sense and to avoid activities including travelling on a cruise line,” he said.
He added political authorities were looking to cruise line officials for action, guidance and flexibility with those passengers.
One day earlier, the CDC quietly updated its website to tell older adults and people with severe medical conditions, such as heart, lung or kidney disease to “stay home as much as possible” and to avoid crowds.
Its advice also urged people to “take actions to reduce your risk of exposure”, but did not specifically mention flying.
Alex Azar, the health and human services secretary, has suggested older Americans and those with health problems should avoid crowds “especially in poorly ventilated spaces”.
In February, a report by The Washington Post claimed US health officials were also overruled by the State Department when Americans who were infected with coronavirus were allowed on a plane with healthy people.
The CDC had argued for keeping 14 people who tested positive for coronavirus in Japan, where they were docked with the quarantined Diamond Princess cruise ship, instead of allowing them to return to the US, the report said.
Although no reason was given for the apparent overruling of health advice for elderly people flying, Donald Trump has repeatedly sought to downplay fears about coronavirus as global stock markets have fallen sharply in recent days.
“They care about one thing; the president’s re-election. And they think that depends on the economy,” Chris Hayes, a MSNBC host and political commentator, said in response to AP’s report.
“And so they want to pretend there’s nothing going on so it doesn’t hurt GDP. It’s sociopathic and dangerous.”
On Friday, Mr Trump visited the CDC in Atlanta, where he defended his administration’s handling of the outbreak and tried to reassure Americans about the government’s strategy.
However, he also drew criticism for calling Washington state governor Jay Inslee a “snake” over criticism of his administration, and for saying he would prefer people who are stuck on a virus-hit cruise ship off San Francisco to not be allowed to come to the US.
“They [health experts] would like to have the people come off, I would rather have the people stay,” the president told reporters.
“I would rather because I like the numbers being where they are. I don't need to have the numbers double because of one ship that wasn’t our fault.”
Mr Trump's comments were taken by some as explicit acknowledgement of his political concerns over the outbreak, which threatens the US economy ahead of the November presidential election.
For most people, coronavirus causes only mild or moderate symptoms, but for others, it can cause pneumonia and be potentially deadly.
As of 10am on Saturday, there have been 100,000 confirmed cases and more than 3,000 deaths from coronavirus, according to the World Health Organisation’s latest figures.
Additional reporting by AP