An open letter - signed by more than 120 organisations around the world - has claimed the extra security could allow child predators to go undetected on the social networking site.
Last year, Mark Zuckerberg revealed plans to make it possible for WhatsApp, Instagram and Messenger users to send messages to each other without switching apps, while all messages would be end-to-end encrypted.
The letter from child protection organisations reads: "At a time when we could be looking to build upon years of sophisticated initiatives, Facebook instead seems inclined to blindfold itself.
"We urge you to recognise and accept that an increased risk of child abuse being facilitated on or by Facebook is not a reasonable trade-off to make.
"Children should not be put in harm's way either as a result of commercial decisions or design choices."
In a statement, Facebook says protecting children online is "critically important" to the plans, and they will be working with governments, organisations, law enforcement and other technology firms to keep them safe.
David Miles, head of safety for Europe, Middle East and Africa, added: "We have led the industry in safeguarding children from exploitation and we are bringing this same commitment and leadership to our work on encryption.
"Over the last few years, we've tripled the size of our safety and security team and now have more than 35,000 people working to protect the people using our platforms.
"We are also continuing to invest billions in safety, including artificial intelligence technology to proactively find and remove harmful content."