The New York City Department of Education advised principals not to use Zoom after privacy concerns about the platform accelerated last week, the department's chief operating officer said late Sunday in an email obtained by CNBC.

The department is now telling schools they should use services provided through Google or Microsoft to connect with students while schools are closed due to the coronavirus pandemic. The message comes after a group of at least three state attorneys general said they were probing the company for potential privacy violations. The Connecticut AG, who announced the probe, said he had been "zoombombed" during a forum about the Census, with hundreds of messages flooding the chat box with profanities.

"We know how hard you and your staff are working to make remote learning a reality for students and families, and appreciate the ways in which you're going above and beyond every day. We also know you share our concern for student safety," DOE COO Ursulina Ramirez said in the email. "That is why we want to clarify guidance and expectations around key elements of remote learning over the coming days, so you can use various online platforms safely and with peace of mind that privacy will be protected for all users — yourselves included."

The DOE is providing resources on how to switch operations from Zoom to Google and Microsoft services. Ramirez said the department is still talking with Zoom about its potential for the DOE to return to the platform in the future. Google has a video calling service called Hangouts, while Microsoft's app Teams is included for organizations that have Office 365 subscriptions.

"The safety and security of our staff and students is at the forefront of every decision we make around remote learning, and for that reason, we have asked schools to transition away from using Zoom as soon as possible," a New York DOE spokesperson told CNBC in a statement. "We know this transition won't happen overnight, and we are supporting our educators with trainings and professional development to get them onto secure tools like Google and Microsoft Teams."

Zoom has seen a flood of new users since the coronavirus pandemic sent students and office workers home and in search of new ways to connect. The company initially took advantage of the new attention, eliminating time limits for free accounts for students and educators. But as consumer flocked to the service, which was originally designed for enterprise customers, a slew of privacy issues were exposed. Certain default settings for conferencing allowed users to access calls they weren't meant to be a part of and the service is not end-to-end encrypted, meaning its calls could be intercepted.

Zoom CEO Eric Yuan began an apology tour last week.

"I really messed up as CEO, and we need to win their trust back," Yuan told The Wall Street Journal in an interview Friday. "This kind of thing shouldn't have happened."

In a blog post last week, the company said it's sharing information on how to set up features that can prevent zoombombing, updated its privacy policy and removed Facebook code that had been sending information to the platform, among other steps.

Other school districts and businesses have moved away from Zoom in light of the privacy concerns as well. Elon Musk's SpaceX banned the service for employees at the end of March, Reuters reported, citing "significant privacy and security concerns," in a memo. A Nevada public school district also decided to end access to Zoom "out of an abundance of caution due to instances of hacking that created unsafe environments for teachers and students," The Washington Post reported.

A Zoom spokesperson said in a statement that the company is talking to New York's DOE about how to use the service safely.

"Zoom is committed to providing educators with the tools and resources they need on a safe and secure platform, and we are in continued dialogue with NYC's Department of Education about how Zoom can be of service during this time," the spokesperson said.

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