Praise be to Allaah.
The basic principle is that the employee is required to
fulfil the conditions stipulated in the contract, so long as those
conditions are not contrary to Islamic teachings. Allah, may He be exalted,
says (interpretation of the meaning): “O you who believe! Fulfill (your)
obligations” [al-Maa’idah 5:1]. And the Prophet (blessings and peace of
Allah be upon him) said: “The Muslims are bound by their conditions, except
a condition that treats something halaal as haraam, or treats something
haraam as halaal.” Narrated by at-Tirmidhi, 1352; classed as saheeh by
Shaykh al-Albaani in Saheeh Sunan at-Tirmidhi.
If the matter is as you say, that your immediate boss is the
one who gave you time off and the company did not tell him to do that, and
the system does not allow that, then it is not permissible for you to take
this break just because your immediate boss agreed, because that is breaking
the terms of your work contract. So you have to return to the company the
money that you took for the time you had a break, even if you have to resort
to some kind of trick, as appropriate; you do not have to tell them what
And Allah knows best.