Mayor Bill de Blasio is asking travelers from 34 states, including Florida where COVID-19 infection rates are high, to quarantine for 14 days after arriving in the city.
Authorities said this week a fifth of all new coronavirus cases in New York City have been from travelers entering the city from other states.
Despite the specter of fines, the checkpoints are more educational than punitive, and officials acknowledged the effort relies on voluntary compliance.
The campaign was criticized for sowing confusion and raising questions about how travelers' personal information would be retained.
He said officials have made more than 86,000 phone calls and sent more than 20,000 text messages to travelers entering New York City from states with high coronavirus infection rates.