The statement, co-signed by Roman Catholic and evangelical Protestant leaders, expressed dismay over rising divorce rates and pledged a recommitment to strengthening traditional marriage.
The Rev. Bob Edgar said several of the NCC's member churches interpreted the document as a "condemnation of same-sex unions rather than an affirmation of marriage," Edgar said in his letter. Edgar said he did not want to be associated with such sentiments.
"I am concerned that in our dangerously fragmented and violent society, misinterpretation of the declaration may be used by some as a pretext for attacks on gay and lesbian persons," Edgar wrote, adding that a "number" of NCC member churches expressed concern about the statement.
The rare joint statement, "A Christian Declaration on Marriage," described marriage as "a holy union of one man and one woman in which they commit, with God's help, to build a loving, life-giving, faithful relationship that will last for a lifetime."
It encourages churches to work harder to support married couples and reduce the nation's divorce rate.
Although the statement made no direct reference to same-sex unions, Richard Land of the Southern Baptist Convention used a Tuesday press conference to reaffirm his church's opposition to gay marriage.
"We certainly don't shy away from asserting that God ordained marriage and that God ordained marriage as between a man and a woman," said Land, president of the Southern Baptists' Ethics and Religious Liberty Commission. "It is a covenantal, lifetime relationship between one man and one woman, not between two people of the same sex."
"It inflamed a situation when the framers of the document wanted it focused on how churches might heal relationships, but it ended up a political document for someone like him to use to attack persons with language that is irresponsible," Edgar said.
Edgar said he should have gotten the entire NCC's approval before signing the document, and said he has learned "incredibly important, helpful and painful" lessons.
The marriage statement was seen by many as a sort of ecumenical trial balloon in an area where the NCC, Catholics and evangelicals could perhaps find some common ground. The NCC is in the process of reinventing itself to attract the participation of Catholics and evangelicals.
Edgar said the flap over the marriage statement does not preclude the three camps from working together in the future. He cited poverty, elderly health care, homelessness and after-school programs as areas where all Christians could agree.
The marriage and same-sex unions question has proven to be deeply divisive in many of the NCC's 36 member churches, with Methodists, Episcopalians and Presbyterians especially torn on the issue of whether to bless same-sex unions.
Edgar said it was "inappropriate" for him to try to speak for the NCC when its own member churches could not agree among themselves.
"On something this important where these churches are dealing with these issues, it was harmful and hurtful for me to have run off in this direction without more consultation," Edgar said.
In addition to Land and Edgar, the statement was signed by Bishop Kevin Mannoia, president of the National Association of Evangelicals, and Bishop Anthony O'Connell, chairman of the Committee on Marriage and Family Life of the National Conference of Catholic Bishops.