About 380 Americans are aboard the Diamond Princess cruise ship, which has docked at Yokohama, a port city southwest of Tokyo.
The aircraft will arrive in Japan late Sunday, and people will be flown to Travis Air Force Base in California, with some passengers continuing to Lackland Air Force Base in Texas, the embassy said in a letter to passengers and crew, posted online Saturday.
After arriving in the U.S., all will need to go through another two weeks of quarantine, the letter said.
Everyone will get a checkup before being allowed on the chartered flight, and those who show symptoms of sickness will not be permitted to board the plane, the embassy said.
"We recognize this has been a stressful experience and we remain dedicated to providing all the support we can and seeing you safely and expeditiously reunited with family and friends in the United States," it said.
So far, 218 people from the ship have tested positive for a new virus. Separately from the cruise ship, Japan has reported 44 cases and one death.
Japan's Health Ministry allowed 11 passengers to disembark Friday, saying that those above 80 years of age, with underlying medical conditions as well as those staying in windowless cabins during the 14-day quarantine can stay at a designated facility on shore.