Excel will load CSV (comma separated value) files and Word will load text and HTML. It depends how complex you want your output to be.
If you need to manipulate the native formats of these Microsoft products then I would suggest that Java is not the best technology to use. You'd be better off with C++, VB or C#.
Failing that (or indeed regardless of that) what you probably want to do is use the APIs provided by Microsoft. They used to call it OLE, but I think it got caught up in the whole ActiveX -> COM/DCOM -> COM+ -> .NET thing. I'm afraid I left Microsoft behind 5 years ago for pastures Java-er so I can't be of more help than that.