Members of the Kirk's General Assembly unanimously backed a motion calling for all documents relating to the Chinook helicopter crash on the Mull of Kintyre on 2nd June 1994 to be "kept in a safe place and not deleted".
A total of 29 people died after the aircraft, which was on its way from RAF Aldergrove near Belfast to Inverness, crashed in a ball of flames.
The Church previously called on the department to "revisit" the incident in 2003.
The Very Rev Dr Alan McDonald, who lives in Cromarty in the Highlands, told the General Assembly the response from the church on Mull of Kintyre and nationally was "much, much appreciated" by the families.
He said: "The MoD is reviewing the records of the accident on the Mull of Kintyre, whether they should be retained or deleted.
"The families are once more feeling very vulnerable and their voices are being ignored again.
"Because of everything that has happened to them over the years, the families simply do not want these records to be deleted.
"Their preference is that the records are kept in a safe place where they can be easily assessed from now on."
Dr McDonald told the General Assembly the MoD had confirmed records, closed in 1995 and 1996, "will be reviewed for release or alternative disposal this year".
The pilots, flight lieutenants Jonathan Tapper and Richard Cook, were accused of gross negligence over the crash.
In 2003, the General Assembly called on the MoD to "revisit" the tragedy while Mr Tapper's father, Michael, watched from the public gallery.
Dr McDonald said the families of the victims felt "encouraged and supported" after the Kirk took up their case.
A fresh review was ordered and in 2011 found the pilots should not have been blamed and the earlier ruling was set aside.
David Hill, a retired MoD helicopter engineer and Dr Susan Phoenix, whose husband Detective Superintendent Ian Phoenix, of the Royal Ulster Constabulary, was killed, recently said the review had no remit to inquire into the actual cause of the crash.
An MoD spokesman said: "The MoD does not destroy records of significant public and historical interest.
"Any records that were closed in 1995 and 1996 will be reviewed this year."
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