over time and working hours related problems

Hi friends
I am totally new in this community, I am a HR Manager of a Manufacturing unit at W.B. Here i am facing a typical problem which needs an industrial lawer's view. In hour Plant workers are working for two shifts in a day that is of 12 hrs each. For 9 hrs ( 8 hrs duty and 1 hr rest) they get usual attendance and for the rest of 3 hrs they get O.T. for single hours, i.e. they get paid for 3 hrs only not for 6 hrs,which they were suppose to get as per Factory Act. Now how we can manage this part. Management is not willing to bear the huge financial burden, buy paying them the double rate. And the workers are also happy as they are earning more. Now what is the way out in legal point of view. Few days back Management has decided to show the workers attendance by making the attendance after 9 hrs work as, they have worked for half hours that is for 1.5 hours and because of that they had received 3 hours O.T. But the problem comes when the question of punching clock came, because those workers needed to punch their card just after completion of 1.5 hrs. And other risks also remained, like after out punch the worker if faces any accidents or so then the situation can become more grave. Now what is the way out how can we legalize this part.
Thanks
R.S. Mukherjee