There are lots of third party libtaries ( mostly commercial) which let you manipulate office documents with or without having MS office available on the system.
There are libraries and XSLFO for generating PDF.
Just google for it. http://www.aspose.com/Default.aspx
is one of these.
iText is opensource component which helps you draw PDF
will help you do the same, using OLE objects provided by microsoft applications.
Also - the new MS office format (for office 2007/ office 12)is open - XML documents, and there is an industry standard ODF format coming up - which you might want to read about.
You could also write java wrappers over VSTO ( visual studio tools for office)