Just a humble suggestion from me, I think for the mean time you can still notify the HOD about their staff's missing punch in. Then release a memo to announce that it is employee's responsibility in monitoring their own attendance and if any missing punch in or punch out in the future, they are liable for the salary deduction as it is deemed as absent case. Else, they should take their own effort in submit in the manual form endorsed by immediate supervisor and HOD to supersede the their absent.

We need an extra level of approval from manager and head of department if employees missed too many punches. If employees missed too many times, then becomes tardiness issue, we usually give letter.