In an alert posted online Saturday, the agency advised air traffic controllers to "stop all departures" to Kennedy, LaGuardia, Newark and other airports in the region.
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The directive also affected Philadelphia International Airport.
The halt was lifted after about 30 minutes. Initially air traffic controllers were warned it could last several hours.
"We have contacted local health authorities and we are developing a plan to quickly sanitize/clean the affected areas," the agency said in a statement Saturday afternoon.
The FAA said the trainee has not been at the facility since Tuesday.
"The center remains open and operational. The FAA has initiated traffic management initiatives for sectors closed during the sanitization process. Flights will be rerouted as part of a longstanding contingency plan to ensure continued operations," the statement continued.
The Associated Press contributed to this report.
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