Is it any xml document or is it a specific xml document with a specific schema?
If it has a known schema and you are actually using the contents of the xml file in your web service method you should change the parameter in the .net service to accept a type bound to the documents root element. This means unmarsheling the file in the java client before sending it. You can use
XML Tools : DTD, XML schema and XML document conversion software tool : XML Utilities to create an XML Schema (xsd) to use with JAXB - XJC to generate object bindings.
On the other hand if it is just a file change the parameter to:
<xs:element xmlns:ns1="http://www.w3.org/2005/05/xmlmime" name="parameterName" ns1:expectedContentTypes="application/xml" type="xs:base64Binary"></xs:element>
If i remember correctly the Java object would translate to byte[], but see what jaxws comes up with.
Once you have created your Port object in the java client do the following to enable
MTOM
BindingProvider bp = ((BindingProvider) port);
SOAPBinding sb = ((SOAPBinding) bp.getBinding());
sb.setMTOMEnabled(true);
bp.getRequestContext().put(JAXWSProperties.MTOM_THRESHOLOD_VALUE, Integer.valueOf(XX));
XX is the size value at which binary data would be sent as a mime attachment. I usually set mine to 0.
HTH
Stephen