This is a little how to for deploying Java x86 via Windows Intune. Unfortunately the default .EXE of Java setup doesn’t work via Windows intune.
What you have to do is, install Java client manually on a test computer. After that you have a folder in %USERPROFILE%\AppData\localLow\Sun\Java\jre1.6.0_31 (this is maybe different. Folder name is equal to the update version > 31)
Copy that folder and place this folder in a temp directory. Go to the Windows intune console and click on the upload link. If ask for the MSI file, go to the temp directory where you placed the Java folder and select the msi file (jre1.6.0_31.msi)
Leave the install arguments by default (empty). Windows Intune will place the /q or /quiet argument in the background automatically for you.
Now, you can deploy Java….
The exact process of uploading software in Windows Intune, see the post about Adobe Reader or install software.