I believe the way a department works is by limiting access to programs to only those users who have that program's department. Any program not in a department will still be accessible to all users. For example, Agency A can have 1 department for program A and all the other programs not in a department. Agency user A with department A will be the only user with access to program A as well as having access to the rest of the other agency programs. However, if all programs in an agency are departments, then users will need access to those departments. As noted by Adele Campbell, the issue here is that users can not have more than 1 department. I think a better fix would be to allow for multiple departments per user vs. creating a new agency...

This seems a very important feature - if a staff at an agency, is assigned to a program Dept., and they still need access to all programs at that agency they are not able to view or edit them.

Program Level Sharing. Multiple departments for users and programs. Currently there is not a way to assign a user a department, ( assigned to one program) and the user have access to all programs in the agency. Communities have to create additional agencies for restricted access, even though it is the same agency, due to department limitations.