The visit by Cardinal Sean Brady and Church of Ireland Archbishop Alan Harper was unannounced, but details have emerged from the prison.
The Belfast Telegraph reports: Senior church and Department of Justice sources confirmed the meeting, which took place three days before Christmas as part of a wider pastoral visit.
Prisoners’ support group Cogus believes the meeting demonstrates the “seriousness” of the churches as attempts continue to end the so-called dirty protest.
In a statement Cogus said the church leaders were told that the Northern Ireland Prison Service has to date “scuppered any chance of having a calm and relaxed wing that allows for prison security and prisoner dignity”.
Several dozen dissident prisoners linked to a number of factions are involved in the jail protest, with some smearing excrement on their cell walls.
The row relates to strip searching and arguments over the controlled movement of prisoners.
But the Belfast Telegraph has been told they asked for “sufficient time” to talk to representatives of the protesters. One source described this as “a priority in the visit”.
It is understood the two were in the prison for several hours, meeting staff, prisoners and chaplains as well as inspecting facilities.