How to track employees entering into the office?

I need to track when employees enter the office.

What sensors should I buy? What ID card should I use? I am planning to use java. Will the card providers provide any API for that?

Best use RF tagged ID cards. Touchless & easy to use. There are also some very good RF tag libraries out there with support for many RF tag providers (better search the java libs first and then decide on the vendor). You will definitely need RF doors (just like in public libraries) or mini RF sensors.