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In case of the Sun/Oracle JVM (JRE/JDK) the SSL certificates are store in this keystore: /etc/java-6-sun/security/cacerts. To update it, use the keytool utility that comes with the JRE/JDK.

Eg.

As you can see from the example, the default keystore password is "changeit".
To verify whether the certificate is actually in the keystore:

If you use OpenJDK, it's quite a bit different though. Install the ca-certificates-java package, put your certificate file into /usr/local/share/ca-certificates with a .crt extension and run update-ca-certificates. The keystore to check/verify is this time here: /etc/ssl/certs/java/cacerts.