I am looking to populate an (associated) array with a command line argument.

The command line would look something like this:

alert -action test -priority '10' -module test_module . . .
The associated array would look like this after the data is read in

flag=(action=test
priority=10
module=Test_Module
It there something availeble in the ksh that works like the Getopt::Long module in perl?

Not really. awk supports associative arrays.

If you tell us what are you trying to do rather than how you want to do it, maybe we can help.