DONCAF has identified one of their teams, Special Programs, to handle all special project cases. These are cases identified by DoD and DON as requiring expeditious handling. Projects include: Presidential Support, North Atlantic Treaty Organization (NATO), Wounded Warrior, and various Special Access Programs.

Special Programs is also responsible for providing clearances on students to all Navy and Marine Corps schools and for all Navy or Marine Corps members attending joint schools or those of other services. Schools may submit their requests for clearance via a memorandum. This memorandum must contain, at a minimum: Command name, Command UIC, Command POC with both DSN and commercial telephone numbers, level of clearance or access required, and the full name and SSN of all students. An e-mail address is not required but may be included. It is helpful if the list is in alphabetical order and numbered. A minimum of four weeks should be allowed for response to a school's list. Lists may be faxed or mailed. Due to the volume, we cannot confirm receipt of faxed lists. School and training commands are strongly encouraged to obtain access to JPAS which will enable them to grant access to students with established eligibility without making a request to DONCAF.