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 state has about half of the total confirmed Covid-19 cases in the entire US.
Mr Trump tweeted that instead of quarantine, a "strong travel advisory" would be issued to New York, New Jersey and Connecticut by the Centers for Disease Control and Prevention (CDC)-
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 did New York's governor say?
New York Governor Andrew Cuomo responded by saying that quarantining the state of New York would be "preposterous" and "anti-American".
"If you said we were geographically restricted from leaving, that would be a lockdown."
He said New York had already implemented "quarantine" measures, such as banning major gatherings and ordering people to remain at home, but that he would oppose any "lockdown" efforts.
"Then we would be Wuhan, China, and that wouldn't make any sense," he told CNN, adding that this would cause the stock market to crash in a way that would make it impossible for the US economy to "recover for months, if not years".
"You would paralyse the financial sector," he said.
He added later: "I don't know how that can be legally enforceable. And from a medical point of view, I don't know what you would be accomplishing.
"But I can tell you, I don't even like the sound of it."
Mr Cuomo also said he would sue nearby Rhode Island if the authorities there continued targeting New Yorkers and threatening to punish them for failing to quarantine.
On Friday, Rhode Island Governor Gina Raimondo deployed National Guard troops to stop cars with a New York licence plate, to remind them of their state's advice that they quarantine.
Soldiers are going door-to-door in coastal vacation communities to ask if any residents have recently visited New York City.
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