Попробуйте так:
Process p = Runtime.getRuntime().exec("sh script.py");
InputStream stdout = p.getInputStream();
InputStream stderr = p.getErrorStream();
InputStreamReader isr = new InputStreamReader(stdout);
InputStreamReader isrerr = new InputStreamReader(stderr);
BufferedReader br = new BufferedReader(isr);
BufferedReader brerr = new BufferedReader(isrerr);
String line = null;
System.out.println("OUTPUT:");
while ((line = br.readLine()) != null)
System.out.println(line);
System.out.println();
System.out.println("ERROR:");
while ((line = brerr.readLine()) != null)
System.out.println(line);
System.out.println();
p.waitFor();
