Currently the MongoDatabase.runCommand variant that does not take a read preference attempts to select a server that can accept writes (standalone, replica set primary, mongos). But this rules out certain use cases: for example, it will not allow a client to sent a replSetInitiate command to an uninitiated replica set member.

The correct behavior is to allow the command to be sent to a server that is directly connected to using the single ServerAddress MongoClient constructor.

A workaround until this is fixed is to use the runCommand variant that accepts a read preference:

database.runCommand(init, ReadPreference.primary());

Thanks to Jeffrey Phillips Freeman for reporting this in https://groups.google.com/forum/#!topic/mongodb-user/Cy8o4iHG6CU.