Companies Act is not an Act to regulate employment, terms and conditions of employment etc. You can introduce rules relating to employment by following the relevant Acts like Industrial Employment (Standing Order) Act and Payment of Wages Act. If you frame standing orders with clauses for late coming and deduction of wages for late coming, and then get it certified by the competent authority, the same will become a rule enforceable by law. In the case of daily rated workers you can decide the hourly rate of wages in accordance with the Minimum Wages Act and start paying for the hours worked, implying deduction for late coming.