I have generated a 4096-bit RSA public key for my application through the following code,

KeyPairGenerator generator = KeyPairGenerator.getInstance("RSA");
generator.initialize(4096);
KeyPair pair = generator.generateKeyPair();

PublicKey publicKey = pair.getPublic();

try (FileOutputStream fos = new FileOutputStream("public.key")) {
    fos.write(publicKey.getEncoded());
}

Using this public key for encryption and the corresponding private key for decryption works as expected.

File publicKeyFile = new File("public.key");
byte[] publicKeyBytes = Files.readAllBytes(publicKeyFile.toPath());
KeyFactory keyFactory = KeyFactory.getInstance("RSA");
EncodedKeySpec publicKeySpec = new X509EncodedKeySpec(publicKeyBytes);
keyFactory.generatePublic(publicKeySpec);

On the system where I generated these keys and tested the encryption and decryption, the Java version is 11 and the class of the publicKey is sun.security.rsa.RSAPublicKeyImpl.

However, in another instance of my application, the provider is different and, the underlying implementation is org.bouncycastle.jcajce.provider.asymmetric.rsa.BCRSAPublicKey. The above code loads the public key just fine and encryption works, but the modulus and exponent are different. This is naturally causing decryption issues.

I have checked that the loaded byte array is the same in both the cases. The Java version of this application is 8, however, using a sun.security.rsa.RSAPublicKeyImpl on Java 8 also works as expected, so I don’t think that is the problem.