I'm not sure exactly what you're asking, but if it's what I think it is, you may need to set the search base to something closer to the root of the tree.
Eg, if you have the base set to something like:
ou=Department1,dc=company,dc=com,o=internet
ou=Department1,o=companyname,c=us
Try stripping off the ou:
dc=company,dc=com,o=internet
o=companyname,c=us
You'll also need to make sure the search scope is sub not one.
The only problem comes up when the uid (or whatever you're using as the login) isn't unique across departments; I'm not sure how you'd handle that. (I assume it's possible, as I know I log into some systems using 'realm/user', I just don't know how you'd map that to something for 'AuthLDAPURL', that you'd be using in this case)
For a breakdown of forming an AuthLDAPURL, see Subversion with Apache and LDAP: Updated or RFC2255