You can use the method described at the following link, which uses WebSphere CLI to import the users
http://awesomedeveloper.blogspot.in/2013/03/creating-lot-of-users-on-websphere.html?cm_mc_uid=15200844713514633392557&cm_mc_sid_50200000=1463811754
We have built a WebSphere Virtual Member Manager based Java Toolkit which can be used to create users even in federated repositories, we will be releasing it soon for reference and community use.
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