"I was shocked and saddened to hear the news of King Charles' illness this evening," he said on Monday night. "My thoughts and prayers, and those of many within our Church, will be with him and his family at this worrying time. We wish His Majesty a full recovery."
The Methodist Church in Ireland also asked for prayers for King Charles.
In a statement, President Rev David Turtle and Lay Leader Mr Tom Wilson, expressed their sadness on learning of Charles' diagnosis of cancer.
The pair asked that Methodists pray for the king, his family and the medical team caring for him as he undergoes treatment.
"We are mindful, too, today of the many people who live with cancer and all who care for them and hold them in our prayers," they added.
In a statement, the Free Presbyterian Church of Ulster, previously led by Rev Ian Paisley, also offered its support to the monarch.
"The thoughts and prayers of the Free Presbyterian Church of Ulster are with His Majesty King Charles III at this time of concern for his health," the church said.
"We think of the beautiful passage of Scripture that was carefully selected for our kings’ coronation service, Colossians 1:9-17, which reminds us that God is sovereign in every situation of life, both as our Creator and Preserver.
"May King Charles and the entire Royal household experience much of God’s merciful and loving care in these difficult days."
The statement was issued in the names of Moderator Rev Samuel Murray, Deputy Moderator Rev Ian Brown and Clerk, Rev John Greer.
Church of Ireland Archbishop of Armagh Rev John McDowell has also offered his support.
“I was saddened to learn of the King’s diagnosis of cancer and ask that the King and his family should be remembered in public prayer and in our private devotions at what will be an anxious time for many people," he said. "The words 'Long live the King' are no empty formula or weary cliché, but are an expression of the heartfelt desire of many people across these islands and far beyond.”
Fr Martin Magill, a priest at St John's Chapel on the Falls Road in Belfast said that he had been praying for King Charles and the royal family on Tuesday morning.
“Because after 35 years as a priest I am very aware that when this diagnosis comes to a family, it is very sharp and the royal family and King Charles will be no exception to that,” he said. “Because at that stage one never knows how it will work out. So I am very much praying for the Charles and his family.”