"I engaged in a lengthy, inappropriate relationship with a woman," he wrote. "While we did not 'know' each other in a Biblical sense, it was nevertheless inappropriately romantic and affectionate."
Calls to Vision Forum Ministries were not returned. In describing its mission, Vision Forum calls the family as "the basic agency of dominion on earth," one that "is under attack from every side today."
Phillips is a leader among conservative Christians who reject birth control and believe that large families are a sign of God's blessings, as seen in his friends Jim Bob and Michelle Duggar's family on TLC's "19 Kids and Counting." He preaches a message of "biblical patriarchy," in which a man is called to "rule over his household" and "the God-ordained and proper sphere of dominion for a wife is the household."
Phillips also takes a dim view of women in the public sphere, saying it is not "the ordinary and fitting role of women to work alongside men as their functional equals" outside the home in business, government and the military.
In 2011, the San Antonio-based ministry reported about $3.3 million in revenue, the most recent available financial records. Phillips received $44,000 in salary from the ministry for a 30-hour workweek, according to the ministry's financial documents.
The related for-profit company was paid $193,176 in 2011 by the nonprofit for "labor and services," according to records.
"I retain ownership of Vision Forum, Inc., a distinct and private company, but consistent with my desires to lead a quiet life focusing on my family and serving as a foot soldier, I will not be giving speeches or running conferences at this time of my life under the banner of VFI or VFM," Phillips wrote.
Dan Busby, president of the Evangelical Council for Financial Accountability a certification agency that does not count Phillips' ministry as a member said it's not unusual to see a related for-profit business next to a nonprofit ministry. For-profits are often used for unrelated business income that would not jeopardize the tax-exempt status of a nonprofit, but it can cause perception issues.
"Segregating the nonprofit and for-profit activities and the financial transactions related to the two types of organizations is a critical aspect of these side-by-side organizations," he said.
Phillips was formerly an attorney for Home School Legal Defense Association. He also founded the San Antonio Independent Christian Film Festival, which former Sen. Rick Santorum attended this year.
In his resignation letter, Phillips sought forgiveness.
"There are no words to describe the magnitude of shame I feel, or grief from the injury I caused my beloved bride and children, both of whom have responded to my repentance with what seems a supernatural love and forgiveness," he wrote. "I thought too highly of myself and behaved without proper accountability."