In a statement on the church website the elders apologised to all the women who've made claims against Hybels.
They said his sins were beyond what he previously admitted and asked for forgiveness over the way they handled the situation.
"To all of the women who have come forward, the church should always follow in Jesus' footsteps to help the wounded find healing, and we are sorry we added to your pain," they said. "That was not our intention, and we regret that it has taken us this long to acknowledge that.
"While we will probably never know with certainty everything that's true about each of your stories, we have no reason not to believe you.
"We are sorry that our initial statements were so insensitive, defensive, and reflexively protective of Bill. We exhort Bill to acknowledge his sin and publicly apologize.
Lead Pastor Heather Larson has also resigned suggesting trust has been broken by the church's leadership and urgent action was required.
Steve Gillen - who has previously worked in numerous roles within Willow Creek - will now take up the role of lead pastor.
Bill Hybels has been accused of numerous counts of sexual misconduct, with the latest claim being made in the New York Times that he indecently touched a former assistant.
While Hybels stood down from church ministry when the allegations first surfaced, he denied wrongdoing but apologised for being "unwise" and potentially misleading people.
Willow Creek has faced much criticism over its handling of the situation. Previous to the allegations being made public an internal investigation cleared him of any misconduct.
Ten women have now come forward with allegations.
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