When I run the application locally it sets the environment variable $status to 4. .... system($cmd;echo $status);

Have you tried that? AFAIK you can't "push" environment variables to the parent process (in this case the shell) on UNIX - i.e. if you set an env variable it will only affect the current process and it's children.

I would probably just print out the value to STDOUT and retrieve it in the perl process using backquotes. Setting variables and then echo()ing them is useless overhead.

my $output = `some-program`;
print "Output from some-program is '$output'";
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that way you're much more flexible and it's easier to debug since you can immediately see the output if you run the program on its own.