This is always understood to be the inner voice of God. Mahatma Gandhiji said he was guided by his inner voice. It is also mistaken for one's soul, which it is not. Conscience is ethical and not spiritual. Conscience is best described as the personality of one's ethical consciousness. The Mother calls conscience the adversary to yoga as it will ask you not to abandon the family. The Gita advises NOT to honour any Dharma but to surrender. So, the Gita too wants the yogi to overlook one's Conscience.
Opinion is of the mind. Attitude is of the vital. Motive is of the being.
Conscience is the being of the ethical personality.
The fundamentalists who want to encourage terrorism and kill their enemies do act on their conscience. A conscience that encourages killing cannot be rational or even ethical.
By relating to the only entity that is conscious; the mind, vital, physical attain their own consciousness.
To be fettered by one's own conscience one becomes a conscientious member of the family or society. But, when one wants to awaken his SOUL and lead a spiritual life, his own conscience will stand in his way. He can make spiritual progress only when he outgrows his conscience.
Consciousness also is mistaken to be spiritual by itself. Consciousness is what exists. It is spiritual only when it is in the spiritual plane.