When loads large amount of records, we can clear the session cache by calling session.clear() every for say 500 records to release the memory in Hibernate Session.

But with EJB3 implmenetation, there is no similar method I can call. What should I do to avoid the memory leak?

2 solutions.
em.getTransaction().commit() does the clear for you (unless you use an Extended persistence context)

( (HibernateEntityManager) em).getSession().clear();