More than 220 staff based at the Kirk's headquarters in Edinburgh had been waiting to discover if they had been succesful a bid for a better deal in a pensions overhaul that would mean the equivalent of a drop in salary of nearly 10% a year.
They were shocked when a letter arrived at the end of last week saying their bid was rejected and they had no choice but to accept the Kirk's terms.
The church previously paid 21% of a worker's salary to the pension pot without the employee needing to contribute.
The Unite union wanted 14% and claimed it had evidence the Kirk has budgeted for that amount.
But, in a bid to tackle a pensions deficit, the church has told staff the non-contributory level would be 11.5%, with an option to increase this by employee and Kirk contributions.
In his letter, central services committee convener Angus Macpherson wrote to staff saying: "I shall be glad to have your agreement to our implementing these changes to pension provision."
Mr Macpherson said he would be grateful for a reply by August 30 and added: "If we do not receive a signed acceptance from you by August 30, I shall write to you before September 30 giving due contractual notice that your employment under existing terms and conditions will end with effect from December 31, 2013, and confirming your employment will continue subject to the revised terms and conditions.
"We should prefer not to proceed in this way and I hope the changes can be implemented by way of agreement."
The central services committee's remit covers departments that carry out the church's central day-to-day service work, including properties, law, IT and human resources.
Last night, the Kirk was accused of railroading through policy despite Unite raising concerns about the changes and their impact on employees.
A Unite spokesman said: "Employees who can't afford to contribute to a pension should not be further penalised by the employer by receiving less contribution to their pension scheme compared to those more able to fund a pension."
One senior Kirk source said: "This has been the wrong way to go about it. You can imagine how people felt when they got this letter. They don't know how it's gong to affect them."
A separate source connected to the Kirk headquarters said: "When you have already had bullying allegations, it does seem to be a heavy-handed management system."
A church spokesman said no rules had been broken, legal obligations were fulfilled and a consultation conducted.
He added: "The church is doing what is has to do legally and contractually for employees."
Unite previously called in the industrial conciliation service Acas to conduct an anonymous staff satisfaction survey amid claims workers were too scared to speak out about their concerns for fear of losing their jobs.
The Kirk said the survey "did indicate a surprisingly significant percentage of people experiencing bullying".
An earlier central services report revealed: "The bullying and harassment issue clearly required to be addressed but it was also important the other findings from the staff survey received attention."
Like many other organisations, the Kirk has been forced to tackle a long-term deficit in its pension provision.
In May it reported a £30 million shortfall in cover of its pension liabilities because of people living longer and volatility in financial markets.
Earlier this month, the Kirk was criticised after it emerged its social care arm is employing hundreds of staff on controversial zero-hours contracts.