Boss,
First of all you have to tackle only your guards at the gate. Ask them to record in and out timings of every person whether there is a punch card system in place or not. Have surprise checks on the accuracy of such recordings. And on weekly or monthly basis prepare a MIS report on these timings, employee wise and circulate the report to the HODs/Bosses for them to view and get shocked. Then you'll automatically get instructions to do certain measures. Why, you may be surprised to receive instructions to keep the gates shut during working hours. First you should have the blessings of your own HOD, if he is one such person he may not like your high handedness.
kumar.s.