Hi Sangeetha,
First of all, do you have any policy on office timings and late comings? If not, announce one soon. Normally, organisations allow a maximum of 10-15 minutes of late coming three to five times during a month. There are also organisations, where there is no grace period allowed and employees are straightaway made to lose either half a day leave or half a day's salary.
In the case of your employee, since he is coming late regularly despite warnings, issue him a letter of warning and also clearly mention to him that for every late coming, half a day salary or half a day leave will be deducted. Also, implement this in totality. Please note that when you have a policy on timings, it should cover all employees in particular grades and should not be randomly used to punish erring employees. Also explain to the employee that "coming to work on time is discipline and staying back late to complete the work is commitment" and these two should never be clubbed.
You have also indicated the level of the employee and the job he is doing etc. Anyway, I hope the above is sufficient for now.
Regards
Krishnan