Delay in "realtime" response

Hello World! I'm constructing an inverted pendulum system, but I'm facing a great delay problem. The time time for response(write to pwm pin, it is) is very long. even with a PID controller, the processes takes about five to ten seconds. it's not sufficient time to balance the shaft. I'm communicating an arduino mega2560 with a matlab 2014b-simulink. I hope someone would be able to solve it. thanks.