Although running AutoIt.exe with the script as a command line argument works, and is probably fine in most situations, I'd like to present this as an alternative.
exec function probably uses ShellExecute rather than just running it. This looks in the registry to find the associated action for
A similar thing can be done in java using
However, AutoIt allows the user to check at install time whether they want the default action to be edit the script file or run it. Dependant on the setting there, this could mean you end up opening the script in a text editor, rather than running it as intended.
ShellExecute (the windows API function) provides an option of what verb to use (default being open). This would allow you to always use the
run verb, but means using the windows function from java, which means a wrapper like this. Although it would mean a lot more effort, you'd be guaranteed it would work on any valid AutoIt installation.