Willow Creek Community Church near Chicago announced on Monday that it plans to launch a new independent investigation into allegations that the Rev. Bill Hybels, the church’s influential founding pastor, sexually harassed female co-workers and a congregant over many years.

The announcement came one day after The New York Times reported on accusations from Pat Baranowski, Mr. Hybels’s former executive assistant. She said that Mr. Hybels had sexually and emotionally abused her while she worked at the church and lived with him and his family in the 1980s.

Heather Larson, one of two top pastors at Willow Creek, said in a statement: “It was heartbreaking yesterday to read about the new allegation against Bill Hybels in The New York Times. We have deep sadness for Ms. Baranowski. The behavior that she has described is reprehensible.”

The church’s other top pastor, the Rev. Steve Carter, resigned on Sunday. He said he could no longer work at Willow Creek in good conscience.