Staff hit out after a pay freeze, which comes as the Kirk reviews the terms and conditions of all 2000 staff at its social care organisation, CrossReach.
CrossReach, which was previously known as the Church of Scotland Board of Social Responsibility, was launched in 2005 and spends £51 million per year.
Teachers, who are registered with the General Teaching Council for Scotland, at the independent Ballikinrain residential school in Balfron, Stirlingshire, argue they now get paid 3.4% less than colleagues in mainstream schools, or up to £800 a year for some staff.
They are also facing cuts to maternity pay and changes to absence leave at the school, which looks after young people with social, emotional and behavioural difficulties.
A group of 13 teachers from Ballikinrain, which was opened in 1968, has now written to Peter Baillie, the chief executive of CrossReach.
The letter states: "We are at the frontline in dealing with extreme behaviour and violence but, despite this, we feel we are all helping to make a difference to some of the most at-risk young boys in society in our care.
"We cannot help but ask why there is not parity of pay between us and our peers in other schools?" A spokesman for the Educational Institute of Scotland teaching union, which represents the staff, said it was seeking a meeting with the Kirk to discuss the changes.
"We are aware of a letter sent by CrossReach which advised of the charity's desire to negotiate revised terms and conditions for the teachers that it employs," the spokesman said. "While we will await formal discussions with the employer to raise specific issues, the EIS shares members' concerns over a number of proposals alluded to in this letter, particularly those referring to proposed detrimental changes to both pension entitlement and other conditions of service."
However, Reverend Syd Graham, convener of the Kirk's Social Care Council, said CrossReach had to respond to budget pressures.
"Like many other social care providers, we are operating in a tight financial climate and facing challenges in relation to income and funding," he said. "The Social Care Council of the Church of Scotland is carrying out a strategic budget review to consider all aspects of its income and expenditure to ensure we are able to sustain and develop viable services to those in need throughout Scotland.
"Employees have been advised of this and a consultation process is taking place with employee representatives on all aspects of the review."
Revd Graham added: "Staff participation in these talks is a priority and integral."
Crossreach supports some of the most vulnerable people in Scotland.