You must remember coming late for work is a disciplinary issue and not just a matter of deduction of salary for the amount of time of being late. It can result in disciplinary action taken against the offender who may face the consequences as mentioned in Section 14 of the Employment Act as follow:
"14. Termination of contract for special reasons.
(1) An employer may, on the grounds of misconduct inconsistent with the fulfilment of the express or implied conditions of his service, after due inquiry:
(a) dismiss without notice the employee; or
(b) downgrade the employee; or
(c ) impose any other lesser punishment as he deems just and fit, and where a punishment of suspension without wages is imposed, it shall not exceed a period of two weeks."
In fact, there are quite a number of discussion in this forum about lateness and the latest is from a query raised by Jess dated 22/10/2010 under Lateness Deduction.
Anyway, if you still think the deduction is not lawful and explanation not reasonable, feel free to make a complaint at the Labour Department.