In an emergency message posted to the embassy's website, the agency said it had received "information about a security threat in Playa del Carmen," and that it is barring government employees from traveling to the resort town.
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Playa del Carmen is a popular destination for American college students traveling for spring break, which many universities observe in March.
This alert bars government employees from traveling to Playa del Carmen, but it doesn't do the same for other U.S. citizens.
The nature of the threat is still unknown, but it comes on the heels of an explosion on the ferry that links Playa del Carmen and Cozumel.
"US citizens must have as much information as possible to make informed travel decisions," State Department spokeswoman Heather Nauert said in a statement Thursday. "We take our obligation to provide information to US citizens seriously as evidenced by the clear, timely, and reliable safety and security information we release worldwide."
Nauert did not specify the nature of the threat. However, the State Department issued a separate emergency message last week notifying US citizens of an undetonated explosive device discovered on a ferry. That incident came about a week after an explosive device detonated on another ferry, injuring several passengers.
US officials have been in touch with Mexican law enforcement officials who are leading the investigation, Nauert said at a news briefing Thursday.
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"Clearly, there is a threat," said Nauert. "We're making Americans aware of that threat so that Americans can protect their own safety and the safety of their families."
Even so, travel experts say you might not want to cancel your spring break trip just yet.
But for spring break travelers, the State Department isn't barring you from going to Playa del Carmen.
"The Mexican government has worked very hard to try to determine what the nature is of the threat that's currently taking place down there," said Nauert. "Americans are certainly welcome to travel there, but please take it into consideration."
Travel consultant, Nicki Squittieri said she's gotten calls about Spring Break travel from curious and concerned clients, but tells them they need to keep in mind this alert doesn't mean big changes for everyone.
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"It's specifically for U.S. government employees and it's specifically for the town of Playa del Carmen which is very small. Doesn't affect the state of Quintana Roo at all. Which currently has the same travel rating as Paris, France, Germany, Italy," said Nicki Squittieri with Legacy Travel.
The State Department alert said if you travel to Playa del Carmen, be aware of your surroundings and purchase travel insurance that covers medical evacuation from Mexico. That's no different from what experts normally encourage.
Squuittieri said the key to staying safe on Spring Break: "Whether they're going to Rome, Paris, or Playa, just be aware of your surroundings. I think my number one tip would be, especially because it's Spring Break right now, don't do anything abroad in any city or country that you wouldn't do at home."
The Mexican government is in charge of the investigation into the security threat. The Mexican officials said Playa del Carmen is safe despite the U.S. travel alert.
CNN contributed to this report.