The city's Department of Education is transitioning schools to Microsoft Teams, which is believed to have the "same capabilities with appropriate security measures in place," TechCrunch reported on Sunday.
"Providing a safe and secure remote learning experience for our students is essential, and upon further review of security concerns, schools should move away from using Zoom as soon as possible," Danielle Filson, a spokesperson for the New York City Department of Education, was quoted as saying.
"There are many new components to remote learning, and we are making real-time decisions in the best interest of our staff and students," Filson said.
After schools in the city closed on March 16, Zoom's popularity as a tool enabling remote learning skyrocketed.
But the platform also started facing criticism as reports of "Zoombombing" and other privacy issues started surfacing from different parts of the country.
"Zoomraiding" or "Zoombombing" refers to a type of online harassment in which hate speech, pornography or other inappropriate content is suddenly flashed by disrupting a video call on Zoom.
Several schools in the US earlier reported that unidentified persons accessed classes conducted through Zoom.
A Massachusetts-based high school reported that while a teacher was conducting an online class using the teleconferencing software Zoom, an unidentified individual(s) dialed into the classroom.
The popular video meeting app courted another controversy when security researchers from Citizen Lab at University of Toronto found that that some Zoom calls were routed through servers in China, along with conference encryption and decryption keys used to secure those calls.
Zooms Founder and CEO Eric Yuan has already apologized for the privacy and security issues being reported in his app that has seen a surge in usage globally as people work from home during lockdowns.
The New York City Department of Education "continues to review and monitor developments with Zoom," said the spokesperson, adding that it will update schools with any changes.