In a speech at the US Justice Department on Friday, Wray said: "When it comes to protecting children, we're at a real inflection point and we risk falling off the cliff".
He said images and video of child pornography traded between abusers on Facebook could be lost if the platform encrypted communications, reports CNN.
"Facebook would transform from the main provider of child exploitation tips to a dream come true for predators and child pornographers: a platform that allows them to find and connect with kids and like-minded criminals with little fear of consequences," Wray told the audience.
Facebook plans to integrate chats among WhatsApp, Messenger and Instagram with end-to-end encryption by 2020.
The Irish Data Protection Commission (DPC) has also warned Facebook over its planned integration of chat services, asking the social media giant to provide it with an "urgent briefing" on the proposals. Facebook CEO Mark Zuckerberg, however, has repeatedly said that end-to-end encryption in messaging is the key.
US Attorney General William Barr and top officials from the UK and Australia on Friday shot a letter to Facebook to abandon its encryption project.
"Companies cannot operate with impunity where lives and the safety of our children is at stake, and if Zuckerberg really has a credible plan to protect Facebook's more than two billion users it's time he let us know what it is," the letter said.
"Risks to public safety from Facebook's proposals are exacerbated in the context of a single platform that would combine inaccessible messaging services with open profiles, providing unique routes for prospective offenders to identify and groom our children," the letter added.
A Facebook spokesperson was quoted as saying that the company "strongly oppose government attempts to build backdoors because they would undermine the privacy and security of people everywhere".
Meanwhile, Facebook received support from over 50 civil liberties groups who urged the company not to end encryption.
"We encourage you to resist calls to create so-called 'backdoors' or 'exceptional access' to the content of users' messages, which will fundamentally weaken encryption and the privacy and security of all users," the groups wrote in an open letter to Facebook.
( With inputs from IANS )