Revd Tom Sinclair was killed in a traffic accident in Edinburgh last night, shortly after leaving a meeting on day three of the Church's annual gathering of its General Assembly.
The 76 year-old minister, a commissioner at the GA this week, was on Waverley Bridge walking across the entrance road to Waverley station, when he was in collision with a car.
Police Scotland has said no arrests have been made in connection with the incident and inquiries are ongoing.
Church of Scotland's Moderator, the Rt Revd John Chalmers remembered Tom and his family in prayers at the start of the Assembly this morning and assured the family that the prayers of the whole Church would continue to be with them.
He said: "The news of Tom's death in such tragic circumstances came as a terrible shock to the General Assembly. Tom Sinclair loved the Church of Scotland and loved General Assembly, we mourn his loss and we commend his wife and family to the care of the community of faith and to the grace God.
"Tom's death is a painful tragedy for his wife and family and will come as real blow to the Presbytery of Lewis which he was still serving as Presbytery Clerk."
Revd Sinclair, originally from Glasgow, was Clerk to the Presbytery of Lewis for over 30 years. He is survived by his wife Pam and a son Jonathan, 43 who lives in Edinburgh.
Mr Sinclair entered the ministry young after studies at Trinity College Glasgow. He completed his probation in Aberdeen Holburn Central with the legendary Dr Knox.
His first parish was Scourie in Sutherland - now known as Eddrachillis. He later moved to Martin's Memorial, Stornoway in the seventies, where he served for almost 30 years.
Church of Scotland minister Revd Hugh Stewart told Premier's Anthony Bushfield during the News Hour that Revd Sinclair was highly respected within the Church:
Meanwhile, final preparations are continuing ahead of this evening's debate on Scotland's independence, despite yesterday's tragedy.
The Church of Scotland has said it's committed to a position of neutrality on the independence referendum.
However, Revd Dr Doug Gay of Glasgow University will speak in favour of a "Yes" vote for independence. Labour MP and shadow foreign secretary Douglas Alexander will represent the pro-Union campaign, Better Together.
Revd Gay told Premier's Des Busteed why the Church has decided to hold the event.
The debate is being chaired by the newly-installed moderator, the Rt Revd John Chalmers.
In a letter ahead of the debate, Revd Chalmers said there would be "much work" for the Church to heal divisions following the vote.
The Church was responding to a letter from the Queen calling on people of faith to "work together for the social good of Scotland whatever the outcome of the independence referendum".
The Church's written response said: "We sincerely appreciate Your Majesty's prayers for the social good of Scotland in this year of referendum.
"Whatever the outcome, we anticipate that there will afterwards be much work for the Church to do in helping people to address the consequences of the referendum and to be reconciled with each other."
The people of Scotland are due to go to the polls on September 18th.