The alert comes the agency says 88 vessels are now either under investigation or observation, but it does not specify how many COVID-19 cases have been reported.
The CDC uses a four-level system to categorize COVID-19 health risks for international travelers. Before Thursday, cruise travel was designated "Level 3: High level of COVID-19," but amid the rapid spread of the omicron variant, the Travel Health Notice level has been updated to Level 4, the highest level.
"The virus that causes COVID-19 spreads easily between people in close quarters onboard ships, and the chance of getting COVID-19 on cruise ships is very high, even if you are fully vaccinated and have received a COVID-19 vaccine booster dose," the warning read.
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Still, neither the CDC nor cruise lines have announced plans to halt cruising.
With the Level 4 warning, the agency is urging cruise travelers to get vaccinated and boosted and wear a mask in shared spaces.
And despite the warning, the CDC still had plans to allow for the expiration of a set of rules that cruises must follow to sail during the pandemic. The regulation, called a conditional sailing order, is scheduled to expire on Jan. 15 to become a voluntary program.
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Most lines require adult passengers to show proof of vaccination against COVID-19. Cruise ships are allowed to relax measures such as mask use if at least 95% of passengers and 95% of crew are fully vaccinated.
Several Florida-based ships have reported outbreaks. The Carnival Freedom was denied entry to Aruba and Bonaire after an undisclosed number of passengers and crew aboard caught the virus.
Some cruise ships have not been allowed to disembark in Mexican ports due to cases reported, bringing to memory the early days of the pandemic when cruise lines negotiated docking plans as ships were being turned away by officials worried about the virus's spread.
The Mexican government said Tuesday it would allow cruise ships with reported coronavirus cases to dock. The country's Health Department said passengers or crew who show no symptoms will be allowed to come ashore normally, while those with symptoms or a positive virus test will be quarantined or given medical care.
The Associated Press contributed to this report.
The video in the media player above was used in a previous report.