while using BAPI BAPI_VENDOR_DELETE it calls XK06 trascation but my concern is that if I call this bapi externally(through JAVA)how can I pass values to the parameters pertaining to the XK06 transaction.
yes you're right, this BAPI won't work with a JCo call, as you will get problems with the dialog.
In this case you need another RFC-Function module which you could call via JayCo and which won't process any dialog.
Unfortunately I don't know one in standard, but you could easily write an RFC-Function module by yourself (which can be accessed than via JCo). All you need to do is to mark the function module as 'rfc' module (during creation of you function) and within the function you need to do an update on table lfa1. The relevant field is 'LOEVM'.