Dear Mr. Swapnil
You can maintain the attendance of your contractor's employees in the same attendance biometric readers which you use for your regular employees. The service provider can make modifications accordingly so that you can generate reports etc., 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 work place for your contractor(s) by allotting table space, computer etc., and may even charge a notional rent. But, do not explicitly involve in their hire, fire, leave, reward, punishment related matters. Please do get their monthly compliance report along with photo copies of PF, ESI, paid challans etc.,