This program will import a private key and associated certficate chain into a Java keystore. Usage is as follows:

java KeyStoreImport keystoreFile certificateFile keyFile alias

keyStoreFile

The file containing the Java keystore

certificateFile

A file containing a chain of concatenated DER-encoded X.509 certificates

keyFile

A file containing a DER-encoded PKCS#8 RSA private key

alias

Alias for the private key and certificate chain in the keystore

Note that the OpenSSL tools may be of help in getting certificates from whatever form you presently have them in into the encodings required by the program.

//
// KeyStoreImport.java
//
// Adds a specified certificate chain and associated RSA private key
// to a Java keystore.
//
// Usage: java KeyStoreImport KEYSTORE CERTS KEY ALIAS
//
//              KEYSTORE is the name of the file containing the Java keystore
//              CERTS is the name of a file containing a chain of concatenated
//                      DER-encoded X.509 certificates
//              KEY is the name of a file containing a DER-encoded PKCS#8 RSA
//                      private key
//              ALIAS is the alias for the private key entry in the keystore
//
// ©Neal Groothuis
// 2006-08-08
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
//
import java.security.*;
import java.security.spec.*;
import java.security.cert.*;
import java.io.*;
import java.util.*;

public class KeyStoreImport {

public static void main(String args[]) {
try {
// Meaningful variable names for the arguments
String keyStoreFileName = args[0];
String certificateChainFileName = args[1];
String privateKeyFileName = args[2];
String entryAlias = args[3];

// Get the password for the keystore.
System.out.println("Keystore password:  ");

String keyStorePassword = (new BufferedReader(
new InputStreamReader(System.in))).readLine();

// Load the keystore
KeyStore keyStore = KeyStore.getInstance("jks");
FileInputStream keyStoreInputStream =
new FileInputStream(keyStoreFileName);
keyStore.load(keyStoreInputStream, keyStorePassword.toCharArray());
keyStoreInputStream.close();

// Load the certificate chain (in X.509 DER encoding).
FileInputStream certificateStream =
new FileInputStream(certificateChainFileName);
CertificateFactory certificateFactory =
CertificateFactory.getInstance("X.509");
// Required because Java is STUPID.  You can't just cast the result
// of toArray to Certificate[].
java.security.cert.Certificate[] chain = {};
chain = certificateFactory.generateCertificates(certificateStream).toArray(chain);
certificateStream.close();

// Load the private key (in PKCS#8 DER encoding).
File keyFile = new File(privateKeyFileName);
byte[] encodedKey = new byte[(int)keyFile.length()];
FileInputStream keyInputStream = new FileInputStream(keyFile);
keyInputStream.read(encodedKey);
keyInputStream.close();
KeyFactory rSAKeyFactory = KeyFactory.getInstance("RSA");
PrivateKey privateKey = rSAKeyFactory.generatePrivate(
new PKCS8EncodedKeySpec(encodedKey));

// Add the new entry
System.out.println("Private key entry password:  ");

String privateKeyEntryPassword = (new BufferedReader(
new InputStreamReader(System.in))).readLine();
keyStore.setEntry(entryAlias,
new KeyStore.PrivateKeyEntry(privateKey, chain),
new KeyStore.PasswordProtection(privateKeyEntryPassword.toCharArray())
);

// Write out the keystore
FileOutputStream keyStoreOutputStream =
new FileOutputStream(keyStoreFileName);
keyStore.store(keyStoreOutputStream, keyStorePassword.toCharArray());
keyStoreOutputStream.close();
}

catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}