There are 47 vacant parishes in the Church of Ireland, according to the Church of Ireland Bishop of Cork.
The Right Rev Paul Colton said the "impossible burden" of paying for the maintenance of physical infrastructure was making the church's core duty - preaching the Gospel - more difficult.
So great was the burden being placed on small minority communities by the State that he feared some could disappear.
"Things cannot go on the way they are," he said.
"The simple reality is that what we have at the moment and what we are trying to sustain is not sustainable in the way in which we are currently addressing it," he said in a statement.
Despite recent preliminary census figures, which showed a healthy growth in the Republic's Church of Ireland population, he said the church faced immense challenges.
Among these he noted rising costs, "including notably insurance premiums and building repairs, which meant that small communities in the diocese could not afford all of the 72 church buildings, not to mention halls, houses and schools, they currently have in our region".
There was what he described as "one of the unforeseen consequences" of new State planning and heritage legislation.
With "the subsequent listing of many of our churches as heritage" this put "an impossible burden on small minority communities." he said.
Those communities could disappear, he warned.
There was also the rapid recent changes in deployment at every level of ministry in the church's life "which has resulted in instability", he said.
However, Bishop Colton believed the church, its ministers, lay and ordained, and parishioners at every level of church life were working hard to sustain its core activities of ministry and partnership with society.
The recent census figures showed that since 1991 there had been an increase in the Church of Ireland population in every county in the Republic apart from Cavan and Monaghan.
However, the figures have been described as "a blunt instrument" when it came to assessing the church's growth.
The census "only records the number of people who claim to be members of the Church of Ireland," noted an editorial in the current Church of Ireland Gazette.
