This is the first time investigators have made that assertion.
Among the apps officials found used by the terrorists were WhatsApp and Telegram, both of which boast of end-to-end encryption that protects the privacy of their users and are difficult to decrypt.
Previously officials have said they found encrypted apps on cell phones recovered from the crime scenes. But they stopped short of saying they believed the apps were used in plotting the attacks.
The officials didn't say what specific evidence shows the apps were used for preparing the attacks. The apps were used in communications among the terrorists for a period before the attacks, the officials say. What was said in encrypted messages may never be known, the officials said.
The investigation is ongoing and far from complete, as investigators work to gather evidence on all of the people involved in plotting the attacks.
Investigators were able to recover some unencrypted communications on at least one cell phone recovered, perhaps an indication of sloppiness by at least one of the attackers, the officials said.
The attackers also used other methods to cover their tracks, including changing cell phone sim cards in an apparent attempt to evade surveillance.
FBI Director James Comey said Wednesday at a terrorism conference at New York Police Department headquarters that "the use of encryption is at the center of terrorist trade craft."
The evidence of encryption use in the Paris attacks is one reason why some U.S. officials including Comey have increased public discussion about the difficulty investigators are finding with encryption.
Among his concern: the FBI's inability to see what was in 109 messages that a American terrorist exchanged with a known ISIS operative in Syria before a shooting attack of a Prophet Mohammed drawing contest in Garland, Texas.
After more than a year of pushing by the FBI, tech companies have resisted making any changes to their encryption standards to allow compliance with court-ordered warrants. Many tech companies boosted their use of encryption following the information made public by Edward Snowden showing that U.S. surveillance programs had broad access to private communications of Americans and people around the world.
CNN has reached out to Whatsapp for comment and is attempting to reach Telegram.