In the Bouncy Castle JCE Provider version 1.55 and earlier the ECIES implementation allowed the use of ECB mode. This mode is regarded as unsafe and support for it has been removed from the provider.

In the Bouncy Castle JCE Provider version 1.55 and earlier the other party DH public key is not fully validated. This can cause issues as invalid keys can be used to reveal details about the other party's private key where static Diffie-Hellman is in use. As of release 1.56 the key parameters are checked on agreement calculation.

In the Bouncy Castle JCE Provider version 1.55 and earlier the DHIES/ECIES CBC mode vulnerable to padding oracle attack. For BC 1.55 and older, in an environment where timings can be easily observed, it is possible with enough observations to identify when the decryption is failing due to padding.

In the Bouncy Castle JCE Provider version 1.55 and earlier the DHIES implementation allowed the use of ECB mode. This mode is regarded as unsafe and support for it has been removed from the provider.

In the Bouncy Castle JCE Provider version 1.55 and earlier the DSA key pair generator generates a weak private key if used with default values. If the JCA key pair generator is not explicitly initialised with DSA parameters, 1.55 and earlier generates a private value assuming a 1024 bit key size. In earlier releases this can be dealt with by explicitly passing parameters to the key pair generator.

In the Bouncy Castle JCE Provider version 1.55 and earlier ECDSA does not fully validate ASN.1 encoding of signature on verification. It is possible to inject extra elements in the sequence making up the signature and still have it validate, which in some cases may allow the introduction of 'invisible' data into a signed structure.

In the Bouncy Castle JCE Provider version 1.55 and earlier DSA signature generation is vulnerable to timing attack. Where timings can be closely observed for the generation of signatures, the lack of blinding in 1.55, or earlier, may allow an attacker to gain information about the signature's k value and ultimately the private value as well.

In the Bouncy Castle JCE Provider version 1.55 and earlier the primary engine class used for AES was AESFastEngine. Due to the highly table driven approach used in the algorithm it turns out that if the data channel on the CPU can be monitored the lookup table accesses are sufficient to leak information on the AES key being used. There was also a leak in AESEngine although it was substantially less. AESEngine has been modified to remove any signs of leakage (testing carried out on Intel X86-64) and is now the primary AES class for the BC JCE provider from 1.56. Use of AESFastEngine is now only recommended where otherwise deemed appropriate.

In Bouncy Castle JCE Provider version 1.55 and earlier the DSA does not fully validate ASN.1 encoding of signature on verification. It is possible to inject extra elements in the sequence making up the signature and still have it validate, which in some cases may allow the introduction of 'invisible' data into a signed structure.

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."

The TLS implementation in the Bouncy Castle Java library before 1.48 and C# library before 1.8 does not properly consider timing side-channel attacks on a noncompliant MAC check operation during the processing of malformed CBC padding, which allows remote attackers to conduct distinguishing attacks and plaintext-recovery attacks via statistical analysis of timing data for crafted packets, a related issue to CVE-2013-0169.

The Legion of the Bouncy Castle Java Cryptography API before release 1.38, as used in Crypto Provider Package before 1.36, has unknown impact and remote attack vectors related to "a Bleichenbacher vulnerability in simple RSA CMS signatures without signed attributes."