In addition to the sources listed below, some university departments (generally in experimental sciences) offer scholarships and fellowships to individual students and postdocs based on academic merit. Applications for graduate study programs in Israeli universities should be sent directly to a specific university department. You can find a list of Academic Departments in Israel here.
If you are interested in a specific area try to locate a specific scientist whose research interests are similar. If you find such a scientist contact him directly. If he/she finds your background suitable he may help you obtain a scholarship. It should be emphasized that such scholarships are generally offered to outstanding students with a good command of English.
Weizmann Institute of Science has a special summer program for undergraduate students: