there is also another way to resolve this issue. lets say you have two tables Table1 and Table2. and it is required to fetch all entries of Table1 not referred/present in Table2 using Criteria query. So go ahead like this...
List list=new ArrayList();
Criteria cr=session.createCriteria(Table1.class);
cr.add(Restrictions.sqlRestriction("this_.id not in (select t2.t1_id from Table2 t2 )"));
.
.
. . . It will perform all the subquery function directly in SQL without including 1000 or more parameters in SQL converted by Hibernate framework. It worked for me. Note: You may need to change SQL portion as per your requirement.