Hi Pasha,
My guess is that the Java trust store needs to be updated for the Java version in use by Eclipse. The CA certificate for your server will have to be added to the Java trust store, which is typically found under $JAVA_HOME/jre/lib/security and is called cacerts.
For more info, see the manual pages for keytool or Import the Certificate as a Trusted Certificate (The Java™ Tutorials > Security Features in Java SE > Exchanging Files).
- Menno