The visit is taking place to mark the 70th anniversary of the Wannsee Conference, a meeting of top Nazi officials in the Berlin suburb of Wannsee on 20 January 1942 that led to the Final Solution.
The delegation includes the Rev Ingolf Ellssel, Chairman of the Pentecostal European Fellowship, and Rev Siegfried Tomazsewski, European Director of Christ for all Nations.
The two-day visit starts on Thursday and will include a wreath-laying ceremony at Yad Vashem's Hall of Remembrance and a prayer service at the Western Wall.
The delegates will meet Israeli cabinet minister Yuli Edelstein and the Chief Rabbinate of Israel. A memorial concert will feature performances by the German Christian Music Academy of Stuttgart.
"The Nazi officials who deliberated at Villa Wannsee over their ghastly plans for exterminating European Jewry were all well-educated, with at least half of them holding doctorate degrees," said Dr Jürgen Bühler, the Executive Director of the International Christian Embassy Jerusalem, which is organising the visit.
"Some were also the sons of Protestant ministers, yet not one of them raised any moral objections to this heinous plot.
"We are here to continue the repentance of our nation for this enormous crime by those who committed mass murder in the name of a wicked ideology."
He added: "The Church in Germany still has so much more to do to amend for our deafening silence in those dark days."