The finding comes as an expert said the Kirk was "in the front line" during bombing raids.
The Register of War Damaged Properties records every incident that struck churches, manses and halls across the country, setting out the date, the extent of damage caused and the cost of repairs to hundreds of properties in communities including Peterhead, Fraserburgh, Aberdeen, Edinburgh, Glasgow, Greenock, Clydebank, Lossiemouth, Kirkcudbright and Kirkcaldy.
The ledger has been kept for years in Edinburgh and will be handed to the National Archives of Scotland to enable historians to investigate it for the first time.
89 cities and towns were bombed across Scotland during the war and figures estimate 2,298 people were killed, and almost 6,000 injured.
Dr Jeremy Crang, a senior lecturer at Edinburgh University, said the register shows the Kirk was "very much in the front line" and provided an "insight into the great challenges and trauma" members faced.
Rev Bill Hogg, convener of the Church of Scotland's committee on church art and architecture, said: "This ledger provides an insight into what church people faced during the Second World War and how they must have felt threatened in their ordinary life.
"Damaged churches must have been quite devastating for communities because they are regarded as places of stability and continuity.
"What this register represents is the attempt the Church was making to keep things going."
Bearsden South Church near Glasgow, now known as Bearsden Cross Church, was rebuilt after being hit by an incendiary bomb dropped by a plane returning from the Clydebank raid.
The ledger states it was: "Totally destroyed - only walls standing."