Since it is possible to send SQL statements to the SQL server using plain old JDBC functionality you can create any database entity you want using DDL statemens "CREATE TABLE" "CREATE PROCEDURE" etc. All you need are sufficient rights on the database.
For creating stored procedures start here in the TSQL help on MSDN:
Create stored procedure[
^]
Still have doubts then leave me a comment.
Best Regards,
Manfred