Dear Mr. Swapnil,
You can maintain the attendance of your contractor's employees in the same attendance biometric readers that you use for your regular employees. The service provider can make modifications accordingly so that you can generate reports separately for regular and contract employees without any mix-up. As a principal employer, you have every right to monitor the books and records of your contractor. In fact, you can allot an exclusive workplace for your contractor(s) by providing table space, a computer, etc., and may even charge a notional rent. However, do not explicitly involve yourself in their hiring, firing, leave, reward, or punishment-related matters. Please ensure you receive their monthly compliance report along with photocopies of PF, ESI, paid challans, etc.