Is it permissible for an employee to issue a certificate attesting to the safety of water used in pharmaceutical manufacturing, despite knowing there is a problem with it, at the request of his superior, for submission to regulatory bodies?

The employee's refusal to falsify certificates that contradict the truth is the correct stance, and it is not permissible for him to obey the manager in this, because there is no obedience to a creature in disobedience to the Creator, and because that is an act of cooperation in sin and aggression. Whoever preserves God, God will preserve him in this world and the hereafter. So, whoever is with God, God is with him.