Counseling and Addressing Late Arrival
First, counsel him about the late coming. It might be helpful to have a suitable higher official, with whom he feels comfortable, open, or friendly, talk to him.
Secondly, salary deductions or deducting marks from his performance is not the correct approach unless there is a policy in place. For example, if three times late results in a half-day leave deduction, then follow that policy. If you are deducting leaves as per the policy, please leave the matter there and stop bothering him further.
Consideration of Work Hours
Thirdly, consider the time he is leaving the office. Determine if his job profile requires him to stay late. As an HR person, you should take this into consideration as well, especially since you have only mentioned that he comes late.
Fourthly, ask him if his timings can be adjusted to come in 30/40 minutes later and leave 30/40 minutes later. I have seen this in many companies, especially in the case of ladies when they are pregnant.
Finding Solutions and Enhancing Skills
As an HR person, try to delve into the individual's concerns and find the best possible solutions. Penalizing should be the last option.
Request your company to provide you with good HR and interpersonal training to enhance your skills.
Regards,
Venkata Krishnamohan