What is the religious ruling regarding the money an employee took from a contractor to facilitate the completion of his paperwork, knowing that what he is doing is dubious, and how can he atone for it?

It is not permissible for a worker to accept a gift for performing their obligatory duty unless authorized by the entity they work for, because such gifts are considered "gifts to employees" which are deemed ill-gotten gain (ghulūl). The Prophet, peace and blessings be upon him, said: "Whoever we employ for a task, let him bring its little and its much. Whatever is given to him from it, he may take; and whatever he is prohibited from, he should cease." He also said: "What is wrong with a worker whom I send, and he says: 'This is for you and this was gifted to me!' Why did he not sit in his father's house or his mother's house to see if anything would be gifted to him or not?" To absolve oneself of this, the authorized supervisor must be informed. If he absolves you of it, it is permissible; otherwise, it must be returned to the workplace. The contractor overlooking part of his wage does not make it permissible to accept a gift from him. One must hold oneself accountable and repent to Allah.