Charles wrote to the Chaldean church speaking of his sadness at the "unbearable and barbaric persecution" of religious minorities by Islamic State militants.
The Prince also made a donation to the charity Aid to the Church in Need in the letter which he signed and addressed to Baghdad-based Archbishop Louis Sako, head of the Chaldean Catholic Church.
Persecuted Christians were in his prayers, Charles wrote.
He spoke of the "fervent hope" that the "diabolical evil" come be overcome if the international community continued to help.
Archbishop Sako responded to the letter and said: "Our Christian community in Iraq has endured massacres, atrocities and other human rights abuses by the terrorist armed group calling itself the "Islamic State" (IS), for the reason of their Faith ... we ask your Highness to encourage the international community to preserve the lives and dignity of the huge number of people affected by this disaster."
Clarence House said they would not comment on private correspondence.