The unique messaging service allows its users to send photos and videos to friends that "disappear" after several seconds. Friends can opt to take a screenshot, but the sender is warned in advance.
The FTC claims Snapchat "made multiple misrepresentations" about the app, including the longevity of photos and videos users sent. The agency's complaint cites workarounds users employ to avoid Snapchat's screenshot detection, as well as third-party apps that save photos or videos indefinitely.
The complaint also says Snapchat deceived users on the amount of personal data it collects and how it protects it. The FTC notes a high-profile breach tied to the Find My Friends feature, which exposed the usernames and phone numbers of 4.6 million users.
"If a company markets privacy and security as key selling points in pitching its service to consumers, it is critical that it keep those promises," said FTC Chairwoman Edith Ramirez in a statement.
The complaint also claims Snapchat collected Apple iOS users contact information without permission, and failed to secure the Find My Friends feature despite a warning about a potential exploit.
In January, Snapchat issued an update to fix the exploit.
Snapchat generated buzz last fall after the messaging service turned down a $3 billion acquisition offer from Facebook. The social network giant later scooped up messaging company WhatsApp for $16 billion.
Follow Brett Molina on Twitter: @bam923.