Plans to divest primary schools from the Catholic Church to other patrons are being hindered by unexpected legal complications, including an absence of paperwork between the state and religious authorities over title to land.

Today will see only the second change of patronage under the scheme when Newtownwhite National School outside Ballina, Co Mayo, transfers from the Church of Ireland to Educate Together in a ceremony due to be attended by Taoiseach Enda Kenny.

Educate Together is also opening new primary schools this month in Trim, Co Meath, Tramore, Co Waterford, and Malahide, north Dublin, under the divestment process. However, since these openings were agreed last March the reform process has stalled.

"We would have expected the 2015 list of schools to be agreed by now," said Paul Rowe, chief executive of Educate Together, which promotes a multidenominational ethos, but there had been unexpected hold-ups due to "real estate" problems, including that many schools earmarked for transfer were owned by religious trusts or foundations.

“Our colleagues in the Catholic Church are very keen that this process proceed for very sound strategic reasons,” he said. However, “where this all gets incredibly difficult is that although the State should have a particular lien on these buildings, they have no paperwork to prove it. This was all done on a nod and a wink with the Catholic Church over the years.”

In most cases, he said, the buildings had been capital-funded 85 per cent by the State, while 90-95 per cent of current funding was provided by the State, but there were no formal agreements as “it was never envisaged things would be any different” regarding patronage.

In the case of Newtownwhite NS, he said the Church of Ireland Bishop of Tuam, Killala and Achonry, Dr Patrick Rooke, was "very positive" and facilitory about the change, but "when it came to having the lease for the buildings transferred to the State, it turns out they were vested in a trust", the three members of which had died in the 1930s.

Mr Rowe said this sort of scenario created considerable legal and consultancy costs, and Educate Together calculated that each school opening was costing it about €100,000 in professional hours.

“This kind of structural change requires a properly funded environment. If you look at the water industry. There is a substantial Government funding line supplying that structural change. The difficulty with the divestment process is it’s designed to be a cost-neutral process. We feel that is unrealistic.”

Newtownwhite is the first Church of Ireland school to be divested under the process, and only the second school in all, after two Catholic schools merged in Basin Lane, Dublin last April to allow for an alternative patron.

A primary school patronage survey, commissioned in 2012 by former minister Ruairí Quinn, recommended alternative patrons for 23 out of 38 towns studied.

Schools in Dublin, Wicklow and Mayo are expected to feature in the next round of the divestment process. A spokeswoman for the department said, however, “it is too early at this stage to say where or how many schools might be involved” and discussions were continuing.

Mr Rowe pointed out that there were a number of omissions from the department's long-list, including Athlone and Dundalk, two urban areas which were excluded from the patronage survey despite "substantial demand" on the ground for change. He also noted that there were no multi-denominational schools in Leitrim, Roscommon, Longford, Cavan, Monaghan or Tipperary.

Ninety per cent of the State’s 3,169 primary schools remain under Catholic patronage, and a further 6 per cent are controlled by Protestant churches.