Cardinal Keith Patrick O'Brien and the Moderator of the General Assembly, the Rt Rev David Lunan, are asking churches to use 'The Jerusalem Prayer', a special prayer written by church leaders in Jerusalem that describes the Holy Land as a region in "much in need of peace".
The call marks a worldwide week of prayer and action for Israel and Palestine, launched at an ecumenical service in Jerusalem on Wednesday.
Rev Lunan, who is set to visit the Holy Land as part of an ecumenical delegation, said: "The continuing strife In the Holy Land is a matter of tremendous concern to all Christians and, indeed, to people of all faiths.
"I hope that Church of Scotland congregations across the country will unite in using 'The Jerusalem Prayer' this coming Sunday, that fear and the anxiety of conflict may be replaced with the joy and happiness of peace."
The week, convened by the World Council of Churches, focuses on raising awareness of the Israel-Palestine conflict among churches and the public, and churches are pressing their national leaders to play a more active role in securing a just resolution to the conflict.
Cardinal Keith Patrick O'Brien added his voice to the call for prayer and action, saying: "If there is anywhere where there should be a lasting peace, it is surely in the Holy Land - that place beloved by all Christians and peoples of goodwill, where Jesus handed on his own message of peace.
"Hopefully, our own Catholic congregations will join many others throughout our land in using 'The Jerusalem Prayer' on Sunday, following on the invitation of the Heads of the Churches in Jerusalem that there be a united prayer for peace in the Holy Land from all over the world."
The Jerusalem Prayer asks the Lord for His redemption and peace to heal divisions.
"Our Holy City and our land are much in need of peace," it reads.
"In Your unfathomable mystery and love for all, let the power of Your Redemption and Your Peace transcend all barriers of cultures and religions and fill the hearts of all who serve You here, of both peoples - Israeli and Palestinian - and of all religions."
The prayer also asks for political leaders "courageous enough to sign a treaty [...] that puts an end to the occupation imposed by one people on another, granting freedom to Palestinians, giving security to Israelis and freeing us all from fear".
Jerusalem church leaders are also gathering the responses to an appeal they made in May for churches around the world to send in their wishes and prayers for the region and its believers.
The prayers, sent from as far afield as New Zealand and Cuba, will be used by the churches in Jerusalem throughout the week of action. Some will be read aloud at a ceremony on Sunday in Bethlehem's Manger Square, where a 'Living Clock' will commemorate the 60 years that Palestinians have lived as refugees.