An objection that may be heard very early is that one should obey one’s conscience even if there appears to be a clash between conscience and authority. Indeed, one reads in the Catechism of the Catholic Church that:
1790 A human being must always obey the certain judgement of his conscience. If he were deliberately to act against it, he would condemn himself.
It might appear that “conscience is king”. However, one must enquire into what conscience actually is before one leaps to such a conclusion. Again, from the catechism:
1790 continued. Yet it can happen that moral conscience remains in ignorance and makes erroneous judgements about acts to be performed or already committed.
1778 Conscience is a judgement of reason whereby the human person recognizes the moral quality of a concrete act that he is going to perform, is in the process of performing, or has already completed. In all he says and does, man is obliged to follow faithfully what he knows to be just and right. It is by the judgement of his conscience that man perceives and recognizes the prescriptions of the divine law:
So, conscience can be in error; conscience can be in ignorance. The key observation is that conscience is a judgement of the practical reason ordered to the assessment of the morality of particular concrete actions, not a speculative faculty of the intellect ordered to the assessment of the moral status of classes of action. Conscience needs to be taught the general principles by which it may judge the morality of particular concrete actions. If the inputs to conscience are wrong, the outputs will be too. As the saying goes: “Garbage in; garbage out”.
So, for example, it is not for the conscience to determine that the proposition “the direct killing of an innocent person” is right or wrong; the intellect receives this teaching from the natural law and from revelation (and consistently taught by the magisterium of the Church). The conscience is then responsible for determining the moral status of a particular act based upon whether the particular act involves the direct killing of an innocent party.
A conscience that is wrongly formed is a disaster for an individual; one with a malformed conscience on grave matter may fall prey to the situation of being obliged to sin under pain of sin. This is why the correct formation of conscience is so vital to the moral life.
The conscience needs to be formed throughout one’s life. As the Catechism puts it:
1783 Conscience must be informed and moral judgment enlightened. A well-formed conscience is upright and truthful. It formulates its judgments according to reason, in conformity with the true good willed by the wisdom of the Creator. The education of conscience is indispensable for human beings who are subjected to negative influences and tempted by sin to prefer their own judgment and to reject authoritative teachings.
1784 The education of the conscience is a lifelong task. From the earliest years, it awakens the child to the knowledge and practice of the interior law recognized by conscience. Prudent education teaches virtue; it prevents or cures fear, selfishness and pride, resentment arising from guilt, and feelings of complacency, born of human weakness and faults. The education of the conscience guarantees freedom and engenders peace of heart.
1785 In the formation of conscience the Word of God is the light for our path, we must assimilate it in faith and prayer and put it into practice. We must also examine our conscience before the Lord's Cross. We are assisted by the gifts of the Holy Spirit, aided by the witness or advice of others and guided by the authoritative teaching of the Church.
Parents, teachers, friends and many more participate in the formation of conscience. The most reliable teacher is the magisterium of the Church; the authoritative guide to the content of the deposit of faith and to prudential judgements concerning morality. If one finds oneself in a situation where conscience disagrees with a teaching of the Church, the obligation is to learn from the Church rather than to accuse the Church of error.
For a detailed exposition of conscience, the old manuals on moral theology can be very helpful. For example: take a look at Question 4 of Volume I of “Moral Theology” by McHugh & Callan. Nearly eighty pages are devoted to an in depth treatment of conscience. See also Veritatis splendor 62-64.