It would be easier if we could see the python line which runs the system call.
A possible solution to your problem is to start the system call without waiting for it's completion, using
subprocess.Popen (see
http://docs.python.org/lib/node533.html). Then, once you have a child process running, print it's output with a loop, like this
child = Popen(...)
for line in child.stdout:
print line