His boss tells him to accept work from contractors that is contrary to the required specifications
Question

                I work in a government department as an engineer and I have to accept the work of the contractors. Sometimes there is some shortfall in the specifications, so I tell my boss at work, who in turn tells his boss who is in charge of the department, and he gives instructions to overlook it and accept the work. What should I do from the shar‘i point of view if I obey my boss in this matter?.
Praise be to Allah.
      If an employee is entrusted with some work, then what he 
      must do is fulfil that trust properly, because Allah says (interpretation 
      of the meaning):

    “Verily, Allaah commands that you should render back the 
    trusts to those, to whom they are due”

    [al-Nisa’ 4:58]. 

    And the Prophet (blessings and peace of Allah be upon him) 
    said: “Allah loves, when one of you does something, for him to do it well.” 
    Classed as saheeh by al-Albaani in Silsilah al-Ahaadeeth al-Saheehah, 
    1113. 

    Based on that, if this overlooking of specifications is 
    something minor that is usually overlooked in contractors’ work, there is 
    nothing wrong with overlooking it. 

    But if it is very different from what is required, to the 
    extent that it may be regarded as deception or corruption, it is not 
    permissible to accept the work from the contractor unless one writes a 
    report of the shortcomings in which the contractor did not adhere to the 
    specifications. 

    Even if in this case your boss instructs you to overlook it 
    and accept the work, it is not permissible for you to obey him, because he 
    is instructing you to deceive and lie, and the Prophet (blessings and peace 
    of Allah be upon him) said: “There is no obedience to any created being if 
    it involves disobedience to Allah, may He be glorified and exalted.” 
    Narrated by Ahmad (1098); classed as saheeh by al-Albaani in Silsilah 
    al-Ahaadeeth al-Saheehah, 197 

    If you can refer the matter to those responsible so that they 
    may take appropriate measures, that will be a good thing. But if you are 
    afraid that one of them may harm you, then it is sufficient to refuse to 
    accept the work unless the faulty specifications are recorded. Then you will 
    have done what is required of you in your work, so that you will not be 
    accused of cheating or making a deal with the contractor later on. 

    It should be noted that if a person seeks to please Allah by 
    angering people, Allah will be pleased with him and will make the people 
    pleased with him. 

    So strive to please Allah, may He be exalted, and do not fear 
    the blame of anyone for the sake of Allah. 

    “And whosoever fears Allaah and keeps his duty to Him, He 
    will make a way for him to get out (from every difficulty).

    3. And He will provide him from (sources) he never could 
    imagine. And whosoever puts his trust in Allaah, then He will suffice him. 
    Verily, Allaah will accomplish his purpose”

    [al-Talaaq 65:2-3]
We ask Allah to help and 
    guide you. 
And Allah knows best.