The warning comes as Microsoft gears up to launch the next version of Active Directory when it releases Windows .net later this year.
Implementing AD is optional in Windows 2000 but the directory will become the heart of Windows .net.
AD is a centralised directory that contains information about users' resources and security permissions that can be interrogated by applications to assist network management. It also contains data about hardware such as routers and servers and forms a major repository for systems management.
Mike Davis, a senior research analyst at Butler Group, said, "The problems can be partly put down to the way companies approach Active Directory. It requires careful planning because if changes have to be made it often means scrapping the existing system and starting again."
Better support is essential if Microsoft is to succeed in making AD the directory of directories in a multiplatform network, Davis added.
Some suppliers that write software to help users roll out AD have also voiced concerns about its costs.