Francis told a conference of Italian bishops in a video message that priests must inform Catholic consciences but not replace them.
The Joy Of Love immediately sparked controversy when released in April 2016 because it cautiously opened the door to letting civilly remarried Catholics receive Communion.
Francis reaffirmed the centrality of The Joy Of Love which has divided the Church as its guide to Catholic couples trying to navigate complicated family situations.
Church teaching holds that unless these Catholics obtain an annulment - a decree declaring their first marriage invalid - they cannot receive the sacraments since they are seen as committing adultery.
But although Francis did not give these Catholics an automatic pass, he suggested that bishops and priests could do so case by case, with the couples' "well-formed" consciences as the guide.
Conservatives accused Francis of sowing confusion and undermining the Church's teaching on the indissolubility of marriage.
Four prominent cardinals formally asked for a clarification to five "dubia," or doubts, they said were prompted by the document, and a group of traditionalist and conservative priests and scholars formally accused Francis of spreading heresy.
Cardinal Gerhard Mueller, whom Francis recently removed as the Vatican's chief doctrinal watchdog, did not join the four "dubia" cardinals or the heresy accusers.
But he warned in a recent book preface that "schismatic temptations and dogmatic confusion" were sown as a result of the debate over the document and said such confusion was "dangerous for the unity of the Church."
Cardinal Mueller sought to offer his own interpretation - that The Joy Of Love can only be read as a continuity of the traditional teaching on marriage - offering what he said was his own "contribution to re-establishing peace in the Church."
