Hi Kumar,
Which user/schema owns your application's tables? It sounds like they may have been put in the system schema by mistake, instead of in a separate application schema, so you may need to move them. You may need to create a user/schema, grant it privileges to create tables, indexes and constraints, then re-create your tables (with PKs) in this schema. Check the HSQLDB documentation or get your DBA to help with this.
Which user are you using to connect to your database? This should be a user that owns (or has access to) these tables,
not the system user/schema. Normally, you would have one user that owns the tables i.e. the user who created them, plus another user who can SELECT/INSERT/UPDATE/DELETE the data in these tables, which you would use for your application's database connection. This allows you to restrict what the application user can do e.g. you might not give this user permission to delete data, or you might set up a user who can only SELECT data, but cannot change anything.
But right now, just focus on making sure the tables are in a non-system user's schema, and then connect to the database via that user.
Please give your tables a primary key. They are not properly defined if you do not do that, and Hibernate will have problems identifying records uniquely if you cannot tell it how to identify the records. This is not an optional feature, it is fundamental to how relational databases work.
Basically, Hibernate needs to know the correct user/schema to connect to, and how to identify individual records uniquely in the database tables inside that schema. Right now, it seems like neither of these things is properly defined, which is probably why you are having problems.
You really need to get some help from a competent database designer or your DBA to resolve these issues, because from what you tell us, your current database design is not a proper basis for developing any kind of database application. And get a book on basic relational database design so you can spot these problems when somebody else gives you a bad database design in future e.g. having no keys is a
really big warning sign!
Good luck!