Instruction on the site say, "You are downloading 4.6 million users' phone number information, along with their usernames. People tend to use the same username around the web so you can use this information to find phone number information associated with Facebook and Twitter accounts, or simply to figure out the phone numbers of people you wish to get in touch with."
The social media firm said it updated its app for Andriod and iOS with a tweak that allows users to opt out of linking their phone numbers with their usernames.
(Watch: Snapchat offers app to opt out of 'find friends' feature)
"Our team continues to make improvements to the Snapchat service to prevent future attempts to abuse our API," the blog post said.
The app is popular among teens because it provides a sense of privacy and allows the photos they post online to disappear within seconds.
Launched in 2011, the app had more than 13 million users in October, according to the latest estimates from Nielsen statistics. Collectively, users receive 400 million "snaps" per day, according to Snapchat, based in Venice, Calif.
—By CNBC's Karma Allen. Follow him on Twitter @iam_karma.