Federal Aviation Administration figures show controllers in the New York City region make one error per 40,000 flight operations and the national average is one error per 84,000 operations, the New York Post reported Monday.
New York's rate is also higher than the error rate at other large metropolitan airports, the newspaper said.
Controllers say many of the mistakes result from trying to manage too much air traffic in too small a space.
Of the area's three airports, Kennedy handles the most flight operations, with an average of 1,292 daily. Newark follows with 1,168 and La Guardia with 1,164.
The FAA says it has increased its monitoring of controller errors by encouraging them to report mistakes that might otherwise go unnoticed.
In an agreement with the controllers' union two years ago, the FAA agreed not to punish self-reported air-control mistakes.
"We believe increased reporting will result in an even safer aviation system," the agency said in a statement.