Fr Brendan Gatt told The Sunday Times the Eucharist can be withheld only when someone has been excommunicated and the case has been made public.
"These are considered extreme circumstances, when, for instance, a Catholic politician starts campaigning for abortion and is excommunicated, and this is announced by the Church," he said.
It for individuals, he said, to decide whether to present themselves for Holy Communion - not for the priest.
The comments were made in the light of a debate sparked by Fr George Dalli, who said last month he would administer Holy Communion to a woman whom he knew was involved in an extramarital relationship.
The bishops later issued a statement highlighting that couples who live together without being married "should not present themselves" for the Eucharist.
The declaration did not actually contradict Fr Dalli's comments, since the bishops encouraged the individuals - not the priests - to make that choice.
They said: "The Catholic Church emphasises that couples who are living together without being married should not present themselves for Holy Communion".
The subtlety of this distinction was missed by many who criticised both Fr Dalli's comments and the bishops' statement.
Fr Dalli was answering a question concerning the case of a particular woman when he said: "I would be abusing my power were I not to administer Holy Communion."
According to theologian Fr Paul Galea, the barrage which ensued after Fr Dalli's comments prompted the bishops to make the statement, guided by a need to uphold the Church's moral teaching and eliminate scandal.
Fr Gatt said a priest is not likely to have a full picture to establish who can receive the Eucharist.
"For instance, one could have killed someone and confessed before he presented himself for communion," he pointed out.
But on top of that, Fr Gatt, said, canon law, like civil law, provided for the right to a good reputation, and refusing communion to someone in a packed church would be undermining that right.
Fr Gatt said: "The weakest people are those who cannot understand... if they see you give Holy Communion liberally, then one can become confused, which is why the bishops issued that statement."
But Fr Dalli made another point when he drew a distinction between the different reasons that led people to cohabit, and insisted he could not condemn a married woman who was abandoned with three children and who found meaning and love in a new relationship.
A 1981 synod document, Familiaris Consortium, deals precisely with this scenario. Towards the end, the document speaks of divorcees, but the situation is analogous to the ones typically seen in Malta: where a separated person has started a new family founded on genuine love.
It contemplates the possibility of couples in this situation receiving Holy Communion with the blessing of the Church. But the situations contemplated are very particular.
One of the conditions, for instance, is that the couple in question restrains its relationship to a platonic one, as much as possible.
Since the controversy created by the comments, more priests have defended the notion of a grey area in a debate characterised by black and white.
"My experience tells me there is a unique individual with her particular history in a unique relationship with another individual, who is also a unique person with a particular history, and their unfathomable personal and joint journey of faith with yet another person, God!" Fr Ġwann Xerri said.
SIC: TomCom