To set up Departments under Setup > Company > Departments, the Department permission must be added to the user's role.
1. Navigate to Setup > Users/Roles > Manage Roles.
2. Edit the role of the user.
3. Under Permissions tab > Lists subtab, add Departments and set Level as needed. See Access Levels for Permissions for more information.
4. Click on Save.
For more information about setting up department, see Creating Departments.