Schaap has been dismissed as pastor of the First Baptist Church of Hammond. The FBI says Schaap is being investigated for an alleged sexual encounter with a minor.
A church spokesperson talked about the investigation and its impact on the church, which is one of the largest of its kind in the country.
"It was starting out to be a difficult decision, but when we found out the facts, we had no choice, we had to do what was right," said Terry Duff, chairman of the Board of Deacons.
The fact, according to a church source, is that First Baptist's hugely popular pastor is accused of having an inappropriate sexual relationship.
"It's broken our hearts," said Duff. "We loved that man, and we trusted that man."
Schaap, 54, has led the mega church's 15,000 regular members since 2001. Until his dismissal this week, he was also the chancellor of Crown Point, Ind.'s Hyles-Anderson College.
"We are all flesh, and I love that man. We all love him. So if he walked on campus right now, I'd give him the biggest hug ever," said Hyles-Anderson College student Marvin Cruz.
"If he deserves to be punished, then that's the law, and he's got to be punished, but as far as the church and everything, it will go on. I don't think things will change," said Hyles-Anderson College student Matthew Martin.
The allegations, say church officials, surfaced about a week ago. Although Schaap has not made any public comments, they say he has admitted to the affair. A criminal investigation is now under way.
In a phone call earlier, a spokesperson for the FBI told ABC7 that: "We became involved from the outset. There is an allegation that the pastor transported an underage minor across state lines for the purpose of having sex. The investigation is ongoing and rapidly unfolding. We have allocated a fair amount of resources to this. We conducted several interviews yesterday and are continuing those today. We expect to have a definitive resolution on whether to go forward with charges within the next week."
"We honestly are going to do everything we can to make sure that this is taken care of and that this will never happen again," said Duff.
Church members have been asked to come forward if they have any information about the situation. During a service Wednesday night at First Baptist Church in Hammond, officials said they did not know if there might be others who were inolved with Schaap.