Archbishop Charles Scicluna on Saturday blessed the tombs in the once-unconsecrated division of the Addolorata Cemetery known as il-Miżbla, while asking for forgiveness for the walls once built to separate the dead.
Celebrating solemn mass marking All Souls' Day, the Archbishop said the cemetery held the bodies of many buried at a time when a "wall separated those who had died in the peace of the Church".
Under the Church interdiction of the 1960s, six Labour Party supporters and others deemed to have violated the Church's teachings were denied a Roman Catholic burial and interred on unconsecrated ground.
"Today that wall has fallen and I ask forgiveness for the walls we built to separate our dead," Mgr Scicluna said.
After the mass, the Archbishop visited the 'Miżbla' area, blessing and praying over several tombs and laying flowers on the tomb of the author and former Deputy Prime Minister Ġużè Ellul Mercer.
Nationalist Party leader Adrian Delia welcomed the Archbishop's move, describing the interdiction as a scourge which had left its mark years later.
In 1988, in a Pastoral Letter for Lent, Archbishop Emeritus Joseph Mercieca had also asked for forgiveness.
During his homily, the Archbishop also spoke of the migrants buried at the cemetery after dying while attempting to cross the Mediterranean, calling for them to be remembered.
"Their loved ones have lost them and do not know where they are," he said. "It is our duty to remember them and care for them. Perhaps we could have taken better care of them while they lived, but the least we can do now is not to forget them."
Twenty-four victims of a 2015 shipwreck that claimed the lives of 850 people are buried in an unmarked grave at Addolorata, having been brought to Malta but never identified.
A memorial was placed on the grave earlier this year, in a ceremony attended by the Archbishop.