Bishop Mehaffey, who was 88, died on Monday evening surrounded by his family.
Dr Mehaffey led the Diocese of Derry and Raphoe for more than 20 years, from his consecration in September 1980 until his retirement in January 2002.
During his time as bishop, he officiated at funerals of many parishioners killed in the Troubles.
In his ministry, Bishop Mehaffey had a close friendship with Bishop Edward Daly was a symbol of the power of partnership and reconciliation.
Pat Hume said: “We are deeply saddened to learn of the death of Dr James Mehaffey, the former Church of Ireland Bishop of Derry and Raphoe.
“Dr Mehaffey was a man of wise counsel, Christian courtesy and civic care throughout his ministry.
“Through his friendship with Dr Edward Daly, they both were the embodiment of peace, partnership and reconciliation on this island.”
“Indeed, he worked with John throughout some of our city and country’s darkest days but never gave up on finding a better way for our traditions and people to live side by side in peace.”“We would like to extend our sincere sympathies to his wife Thelma, his children and wider family circle at this time.”
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