Depending upon your requirements (i.e. frequencey and volume), the FrameMaker Publishing Server version is designed for what you want to do. See:
However, this is a pricey product for the occassional use scenario. Alternate approaches are to use some of the freebie batch (command line) utilities for FM out there, such as:
DZbatcher from Datazone (http://www.miramo.com/english/overview/download.html)
runfm.exe as part of the mif2go demo package (http://www.omsys.com/dcl/download.htm)
DoBatch from cudspan (http://www.freeframers.org/freeware/cud/)
Note: most of these were created for older versions of FM and may or may not work properly with the newer versions.