X509Certificate cert = ...
TBSCertificate tbsCertificate = new TBSCertificate();
Asn1BerDecodeBuffer buf = new Asn1BerDecodeBuffer(cert.getTBSCertificate());
tbsCertificate.decode(buf);
OID SubjectKeyIdentifierOid = new OID("2.5.29.14");
Asn1ObjectIdentifier SubjectKeyIdentifierOId = new Asn1ObjectIdentifier(SubjectKeyIdentifierOid.value);
int len = tbsCertificate.extensions.elements.length;
SignerIdentifier sid = null;
for (int i = 0; i < len; i++) {
  if (tbsCertificate.extensions.elements[i].extnID.equals(SubjectKeyIdentifierOId)) {
    Asn1OctetString extnValue = tbsCertificate.extensions.elements[i].extnValue;
    sid = new SignerIdentifier();
    sid.set_subjectKeyIdentifier(extnValue);
  }
}