The default BKS keystore use an HMAC that is only 16 bits long, which can allow an attacker to compromise the integrity of a BKS keystore. Bouncy Castle release 1.47 changes the BKS format to a format which uses a 160 bit HMAC instead. This applies to any BKS keystore generated prior to BC 1.47. For situations where people need to create the files for legacy reasons a specific keystore type "BKS-V1" was introduced in 1.49. It should be noted that the use of "BKS-V1" is discouraged by the library authors and should only be used where it is otherwise safe to do so, as in where the use of a 16 bit checksum for the file integrity check is not going to cause a security issue in itself.

BouncyCastle TLS prior to version 1.0.3, when configured to use the JCE (Java Cryptography Extension) for cryptographic functions, provides a weak Bleichenbacher oracle when any TLS cipher suite using RSA key exchange is negotiated. An attacker can recover the private key from a vulnerable application. This vulnerability is referred to as "ROBOT."