President Donald Trump has said quarantining New York "will not be necessary", after the state's governor said doing so would be "preposterous".
Mr Trump said the latest decision was taken on the recommendation of the White House Coronavirus Task Force.
The president had earlier said he might impose a quarantine on New York, and parts of New Jersey and Connecticut, to slow the spread of Covid-19.
There are more than 52,000 cases in New York.
The CDC then published a statement urging residents of those three states to "refrain" from all non-essential domestic travel for 14 days.
The agency said the advisory did not apply to "critical infrastructure" service providers, including healthcare professionals and food suppliers.
Speaking to reporters earlier on Saturday about the situation in New York, Mr Trump said: "We'd like to see [it] quarantined because it's a hotspot... I'm thinking about that."
He said it would be aimed at slowing the spread of the virus to other parts of the US.
"They're having problems down in Florida. A lot of New Yorkers are going down. We don't want that," he said.
What's the latest in the US?
With more than 1800 virus-related fatalities, the US death toll remains lower than those in Italy and China. But there are virus hotspots in New York, New Orleans, Detroit and Seattle.
Saturday saw the first death in the US of an infant who had tested positive for coronavirus. The baby died in Chicago.
Of the 112,100 confirmed cases in the US, almost half have been in New York.