system runs your commands using /bin/sh. If /bin/sh is a link to a Bourne shell (it's likely), the error you're seeing will occur. setenv is not a valid Bourne shell command.

You can alter the environment of your Perl script with the %ENV hash:

## untested
{
    local %ENV;
    $ENV{'GENESIS_DIR'}  = '/genesis/customers/ckt-imgs';
    $ENV{'GENESIS_EDIR'} = '/genesis/e90';
    system '/genesis/e90/get/get';
}
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