Dear reik
Welcome to CiteHR.com.
I can understand your predicament, but I do not understand how you could be inviting trouble from CBI or other investigating agency - you should have come up with your specific apprehensions.
I also understand that your boss has delegated this task to you as he does not wants to annoy the union leader.
In your section/department, how do you make attendance ?
Since you have been asked to "mark" it, I reckon it must be in an "Attendance Register" and employees are asked to put their initials everyday of attendance.
Is the Attendance Register meant for your specific section, or the whole deptt./organization ?
In general, how many employees 'sign' it everyday ?
Where is the Attendance Register placed everyday (for making attendance) ?
Is it moved everyday, once the employees have made their attendance (say, after an hour of reporting time) ?
At the end of the month, who sends the attendance data to Finance - Actts./wages/salary deptt. ?
Under whose signature, the data is sent ?
I shall be able to suggest further, when you provide answers to these queries.
Warm regards.