Modern man has a distorted idea about the authority of conscience. It is not absolute in the sense of being free to choose whatever moral course it wishes. Pope John Paul II has the following interesting things to say about this in VS §34:
The question of morality, to which Christ provides the answer, cannot prescind from the issue of freedom. Indeed, it considers that issue central, for there can be no morality without freedom: “It is only in freedom that man can turn to what is good”. But what sort of freedom? The Council, considering our contemporaries who “highly regard” freedom and “assiduously pursue” it, but who “often cultivate it in wrong ways as a licence to do anything they please, even evil”, speaks of “genuine” freedom: “Genuine freedom is an outstanding manifestation of the divine image in man. For God willed to leave man “in the power of his own counsel” (cf. Sir 15:14), so that he would seek his Creator of his own accord and would freely arrive at full and blessed perfection by cleaving to God”. Although each individual has a right to be respected in his own journey in search of the truth, there exists a prior moral obligation, and a grave one at that, to seek the truth and to adhere to it once it is known. As Cardinal John Henry Newman, that outstanding defender of the rights of conscience, forcefully put it: “Conscience has rights because it has duties”.
Certain tendencies in contemporary moral theology, under the influence of the currents of subjectivism and individualism just mentioned, involve novel interpretations of the relationship of freedom to the moral law, human nature and conscience, and propose novel criteria for the moral evaluation of acts. Despite their variety, these tendencies are at one in lessening or even denying the dependence of freedom on truth.
If we wish to undertake a critical discernment of these tendencies — a discernment capable of acknowledging what is legitimate, useful and of value in them, while at the same time pointing out their ambiguities, dangers and errors — we must examine them in the light of the fundamental dependence of freedom upon truth, a dependence which has found its clearest and most authoritative expression in the words of Christ: “You will know the truth, and the truth will set you free” (Jn 8:32). [Italics in original]
Freedom is dependent upon truth, as JPII also said in Fides et Ratio §90 (we looked at this here). But conscience is dependent upon freedom. Consequently conscience is dependent upon truth, and so we see that man has those duties affirmed by Cardinal Newman above. He has a duty to inform his conscience, so that it is conformed to the truth. He has a duty to act in accordance with the truth. He is not free to to do just anything; God did not give us a freedom to do just anything, but rather He gave us freedom to love Him and to obey Him.