Is saying that an employee is "not present" when they are present and aware of it considered a lie?

Lying is forbidden (haram), and it is informing against the reality. What you mentioned to the student falls under this. However, it may be permissible to achieve a benefit or avert a harm that could not be avoided otherwise. If it is not for such a reason, then it is forbidden. And if you were to use allusive speech (tawriya), it would be better, based on the saying of Umar and Ibn Abbas: "Indeed, in allusive speech there is a way out of lying."