Question

Reading Oracle documentation, I see that by default JKS files are encrypted using PBEWithMD5AndTripleDES. While DES alone makes me feel uneasy, MD5 lights a big red light. I’d like to use PBEWithSHA256And256BitAES-CBC-BC or PBEWithSHA256And128bitAES-CBC-BC to encrypt private keys.

Do I have to write new Cryptography Service Provider implementing whole KeyStore interface or is it possible to parametrise the creation of KeyStore (either using plain java or BouncyCastle)?

EDIT:
A little bit of background.

I know that 3DES isn’t broken, just as is MD5 used as KDF (or in PBE). The problem is, that this is the situation for now. For all we know, MD5 may be broken to the level MD4 is broken tomorrow. My application life is at least 10 years, and it’s very likely it’s much more. Somehow I don’t see people after those 10 years delving deep into working crypto code just because it may not be secure. One just needs to look at last few of the big “mishaps” with password leaks to see how likely is that, and that were obvious things to anyone that saw the raw database.

That being said: NSA crypto suite B allows only AES for symmetric encryption, of any kind.
NIST list only SHA-1 and SHA-2 algorithms for HMAC and KDF use, while SHA-1 use is not recommended. Suite B allows only SHA-2 hash functions. Those algorithms are publicly available, so why shouldn’t I use them?

Answer 1

In the end I went with PKCS#8 files encrypted using PBEWithSHA256And256BitAES-CBC-BC

Encryption:

import java.io.FileOutputStream;
import java.io.IOException;
import java.security.AlgorithmParameters;
import java.security.InvalidAlgorithmParameterException;
import java.security.InvalidKeyException;
import java.security.KeyPair;
import java.security.KeyPairGenerator;
import java.security.NoSuchAlgorithmException;
import java.security.NoSuchProviderException;
import java.security.SecureRandom;
import java.security.Security;
import java.security.spec.InvalidKeySpecException;
import java.security.spec.InvalidParameterSpecException;

import javax.crypto.BadPaddingException;
import javax.crypto.Cipher;
import javax.crypto.EncryptedPrivateKeyInfo;
import javax.crypto.IllegalBlockSizeException;
import javax.crypto.NoSuchPaddingException;
import javax.crypto.SecretKey;
import javax.crypto.SecretKeyFactory;
import javax.crypto.spec.PBEKeySpec;
import javax.crypto.spec.PBEParameterSpec;

import org.bouncycastle.asn1.bc.BCObjectIdentifiers;

public class EncodePKCS8 {

/**
 * @param args
 * @throws NoSuchAlgorithmException 
 * @throws InvalidKeySpecException 
 * @throws NoSuchPaddingException 
 * @throws InvalidAlgorithmParameterException 
 * @throws InvalidKeyException 
 * @throws BadPaddingException 
 * @throws IllegalBlockSizeException 
 * @throws InvalidParameterSpecException 
 * @throws IOException 
 * @throws NoSuchProviderException 
 */
public static void main(String[] args) throws NoSuchAlgorithmException,
InvalidKeySpecException, NoSuchPaddingException, InvalidKeyException,
InvalidAlgorithmParameterException, IllegalBlockSizeException, BadPaddingException,
InvalidParameterSpecException, IOException, NoSuchProviderException
{
    // before we can do anything with BouncyCastle we have to register its provider
    Security.addProvider(new org.bouncycastle.jce.provider.BouncyCastleProvider());

    String password = "Very long and complex password";

    // generate RSA key pair
    KeyPairGenerator keyPairGenerator = KeyPairGenerator.getInstance("RSA");
    keyPairGenerator.initialize(2048);
    KeyPair keyPair = keyPairGenerator.genKeyPair();

    byte[] encryptedPkcs8 = encryptPrivateKey(password, keyPair);

    FileOutputStream fos = new FileOutputStream("privkey.p8");
    fos.write(encryptedPkcs8);
    fos.close();

    return;
}

private static byte[] encryptPrivateKey(String password, KeyPair keyPair)
    throws InvalidKeyException, NoSuchAlgorithmException, NoSuchProviderException,
    InvalidKeySpecException, NoSuchPaddingException,
    InvalidAlgorithmParameterException, IllegalBlockSizeException,
    BadPaddingException, InvalidParameterSpecException, IOException
{
    int count = 100000; // hash iteration count, best to leave at default or increase
    return encryptPrivateKey(password, keyPair, count);
}

/**
 * 
 * @param password
 * @param keyPair
 * @param count
 * @return PKCS#8 encoded, encrypted keyPair
 * @throws NoSuchAlgorithmException
 * @throws NoSuchProviderException
 * @throws InvalidKeySpecException
 * @throws NoSuchPaddingException
 * @throws InvalidKeyException
 * @throws InvalidAlgorithmParameterException
 * @throws IllegalBlockSizeException
 * @throws BadPaddingException
 * @throws InvalidParameterSpecException
 * @throws IOException
 */
private static byte[] encryptPrivateKey(String password, 
        KeyPair keyPair, int count) throws NoSuchAlgorithmException,
        NoSuchProviderException, InvalidKeySpecException,
        NoSuchPaddingException, InvalidKeyException,
        InvalidAlgorithmParameterException, IllegalBlockSizeException,
        BadPaddingException, InvalidParameterSpecException, IOException
{
    // extract the encoded private key, this is an unencrypted PKCS#8 private key
        byte[] encodedprivkey = keyPair.getPrivate().getEncoded();

        // Use a PasswordBasedEncryption (PBE) algorithm, OID of this algorithm will be saved
        // in the PKCS#8 file, so changing it (when more standard algorithm or safer
        // algorithm is available) doesn't break backwards compatibility.
        // In other words, decryptor doesn't need to know the algorithm before it will be
        // able to decrypt the PKCS#8 object.
        String encAlg = BCObjectIdentifiers.bc_pbe_sha256_pkcs12_aes256_cbc.getId();

        SecureRandom random = new SecureRandom();
        byte[] salt = new byte[16];
        random.nextBytes(salt);

        // Create PBE parameter set
        PBEParameterSpec pbeParamSpec = new PBEParameterSpec(salt, count);
        PBEKeySpec pbeKeySpec = new PBEKeySpec(password.toCharArray());
        SecretKeyFactory keyFac = SecretKeyFactory.getInstance(encAlg, "BC");
        SecretKey pbeKey = keyFac.generateSecret(pbeKeySpec);

        Cipher pbeCipher = Cipher.getInstance(encAlg, "BC");

        // Initialize PBE Cipher with key and parameters
        pbeCipher.init(Cipher.ENCRYPT_MODE, pbeKey, pbeParamSpec);

        // Encrypt the encoded Private Key with the PBE key
        byte[] ciphertext = pbeCipher.doFinal(encodedprivkey);

        // Now construct  PKCS #8 EncryptedPrivateKeyInfo object
        AlgorithmParameters algparms = AlgorithmParameters.getInstance(encAlg, "BC");
        algparms.init(pbeParamSpec);
        EncryptedPrivateKeyInfo encinfo = new EncryptedPrivateKeyInfo(algparms, ciphertext);

        // DER encoded PKCS#8 encrypted key
        byte[] encryptedPkcs8 = encinfo.getEncoded();

        return encryptedPkcs8;
    }
}

Decryption:

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.security.AlgorithmParameters;
import java.security.InvalidAlgorithmParameterException;
import java.security.InvalidKeyException;
import java.security.Key;
import java.security.KeyFactory;
import java.security.NoSuchAlgorithmException;
import java.security.PrivateKey;
import java.security.PublicKey;
import java.security.Security;
import java.security.interfaces.RSAKey;
import java.security.interfaces.RSAPrivateCrtKey;
import java.security.interfaces.RSAPublicKey;
import java.security.spec.InvalidKeySpecException;
import java.security.spec.KeySpec;
import java.security.spec.RSAPublicKeySpec;

import javax.crypto.Cipher;
import javax.crypto.EncryptedPrivateKeyInfo;
import javax.crypto.NoSuchPaddingException;
import javax.crypto.SecretKeyFactory;
import javax.crypto.spec.PBEKeySpec;

public class DecodePKCS8 {

    /**
     * @param args
     * @throws IOException 
     * @throws NoSuchPaddingException When file is corrupted
     * @throws NoSuchAlgorithmException When no BC provider has been loaded 
     * @throws InvalidKeySpecException When decryption of file failed
     * @throws InvalidAlgorithmParameterException When file is corrupted
     * @throws InvalidKeyException When Unlimited cryptography extensions are not installed
     */
    public static void main(String[] args) throws
    IOException, NoSuchAlgorithmException, NoSuchPaddingException,
    InvalidKeySpecException, InvalidKeyException, InvalidAlgorithmParameterException
    {
        // before we can do anything with BouncyCastle we have to register its provider
        Security.addProvider(new org.bouncycastle.jce.provider.BouncyCastleProvider());

        String password = "Very long and complex password";

        // read DER encoded key from files
        byte[] encodedprivkey = getFileBytes("privkey.p8");

        // this is a encoded PKCS#8 encrypted private key
        EncryptedPrivateKeyInfo ePKInfo = new EncryptedPrivateKeyInfo(encodedprivkey);

        // first we have to read algorithm name and parameters (salt, iterations) used
        // to encrypt the file
        Cipher cipher = Cipher.getInstance(ePKInfo.getAlgName());
        PBEKeySpec pbeKeySpec = new PBEKeySpec(password.toCharArray());

        SecretKeyFactory skFac = SecretKeyFactory.getInstance(ePKInfo
                .getAlgName());
        Key pbeKey = skFac.generateSecret(pbeKeySpec);

        // Extract the iteration count and the salt
        AlgorithmParameters algParams = ePKInfo.getAlgParameters();
        cipher.init(Cipher.DECRYPT_MODE, pbeKey, algParams);

        // Decrypt the encryped private key into a PKCS8EncodedKeySpec
        KeySpec pkcs8KeySpec = ePKInfo.getKeySpec(cipher);

        // Now retrieve the RSA Public and private keys by using an
        // RSA key factory.
        KeyFactory rsaKeyFac = KeyFactory.getInstance("RSA");
        // First get the private key
        PrivateKey rsaPriv = rsaKeyFac.generatePrivate(pkcs8KeySpec);
        // Now derive the RSA public key from the private key
        RSAPublicKeySpec rsaPubKeySpec = new RSAPublicKeySpec(((RSAKey) rsaPriv).getModulus(),
                ((RSAPrivateCrtKey) rsaPriv).getPublicExponent());
        PublicKey rsaPubKey = (RSAPublicKey) rsaKeyFac.generatePublic(rsaPubKeySpec);

    System.out.println("Key extracted, public part: " + rsaPubKey);
    }

    private static byte[] getFileBytes(String path)
    {
        File f = new File(path);
        int sizecontent = ((int) f.length()); // no key file will ever be bigger than 4GiB...
        byte[] data = new byte[sizecontent];
        try 
            {
            FileInputStream freader = new FileInputStream(f);
            freader.read(data, 0, sizecontent) ;
            freader.close();
            return data;
            }
        catch(IOException ioe)
        {
            System.out.println(ioe.toString());
            return null;
        }
    }
}