The Unite union said the action was being planned over a pay deal it believes is unfair.
Up to 80 out of the 227 staff based at the Kirk's administrative headquarters in George Street in Edinburgh are being balloted on taking industrial action in the coming weeks. It could affect the General Assembly, for which about 1000 Church leaders meet at The Mound in the Scottish capital.
The union said the division of a pay package that gave all workers the same one-off £300 payment as an annual rise regardless of rank should be abandoned and payments made according to salary level.
Unite said the decision had been forced on its members, and the Church confirmed it had been contacted by the union over the possible industrial action.
Such action could cause logistical problems during the General Assembly, when the eyes of the world will be following debates on issues including the allowing gay clergy.
The Church said it was contractually obliged to settle the negotiations after months of deadlock so workers could receive the payment.
A spokeswoman for Unite said: "We consulted every employee, not just our members. The overall opinion was that more money should go to those at the lower end of the pay scale than those at the top of it. The members were not satisfied with the way the decision was imposed."
The union claimed staff backed a plan to share the overall pay rise fund of £80,000 with lower-paid staff receiving £350, middle earners £300, and high-bracket workers £250.
It is understood wages range from about £17,000 to £70,000.
The Church of Scotland's Central Services Committee Vice-Convener Philip Craig said: "The committee's decision to award its 200 staff a £300 annual salary increase this year is equivalent to a 1.7% annual pay rise for lower paid staff, compared to 0.4% for higher earners.
"The award followed four months of negotiations with Unite, which the committee believes were carried out in good faith by all sides. The £300 pay award is £50 per year lower than Unite sought for lower-paid staff but the committee felt it had to make a decision so all staff could benefit from the pay rise, which is backdated to January 1.
"We are disappointed Unite intend to hold a strike ballot and we remain willing to engage constructively with the union and with staff on this matter."
In a letter to staff, Mr Craig wrote: "After careful consideration, the committee felt that staff at all levels had made a valuable contribution so ultimately took the view that staff should receive the same monetary amount.
"The committee is very sympathetic to Unite's view that the needs of those on lower grades should be recognised and it is satisfied the award means those staff will receive a proportionately higher percentage rise than those on higher grades."
The Central Services Committee's remit covers departments that carry out the central day-to-day service work of the Church, including administration of its law IT and human resources departments.