Speaking to CNN Friday, Falwell confirmed the emails were authentic, but said they lacked critical context.
"I would have to see the full thread to see what I was talking about," he told CNN.
There were counterprotesters as well, including one who held a sign that said "Keep Jerry as president. Change my mind."
Falwell told CNN on Friday that he was not bothered by the protests.
"I just think that what college is all about, letting kids speak their minds," Falwell said. "It shows how healthy Liberty is as a free and open university that protest like that can take place, and I am proud of it."
Reuters this week reported on dozens of emails, some of which contain offensive language, Falwell exchanged over the past decade, including one where he reportedly called a then-student "emotionally imbalanced" and "physically retarded" in 2010.
In one 2015 email, Reuters quotes Falwell as lashing out about students parking in private lots instead of paying parking fees to Liberty: "These students need to learn to play by the rules or they can go to another college. I'm tired of this crap."
And when a parent wrote out of concern for her student being moved from a dorm due to construction, Reuters says Falwell wrote to other administrators, saying: "Tell them, if they keep complaining, we'll tear them down over Thanksgiving break!"
In other emails reported by Reuters, Falwell calls a university official "a bag of hot air" who "couldn't spell the word 'profit.'" He reportedly calls another official "a half-wit and easy to manipulate." And said of a third official that he should only be "involved in something if you want it not to work."
Falwell told CNN that the emails had been "stolen," and defended his comments about Liberty's chief of police.
"Anybody can pick out an email," Falwell said. "Reuters is still publishing stolen emails. All those emails have been stolen from Liberty's servers. The chief of police, why I said what I said about him is that he was going to oppose the idea of making concealed carry allowable on campus for students 21 and older."
The campus police chief in question has not responded to CNN's request for comment.
Responding to the e-mail about a student's emotional and physical health, Falwell told CNN: "I don't know about the others (emails). I don't even know what physically retarded means. I would have to see the context and top of the thread to see what I was talking about. I don't remember what the other emails were about."
A spokesman for Liberty University declined to comment on any of the emails to CNN.
"I think it's all a political-based attack by people who wanted to run the school for themselves," Falwell told CNN on Friday.
The FBI declined to comment when asked about Falwell's concerns.
Asked about his tumultuous week, Falwell said he was "very much enjoying" it.
"I don't believe there is any such thing as bad publicity and the worst thing that can happen to anybody who's trying to lead a national organization is to be ignored,' Falwell said.
"I really don't care what they say. In the end they are going to look like fools, so I am actually very much enjoying this week. That comes from 57 years of me being in the crosshairs, first as my father's son and then as president of Liberty. To me, it's a sign that I am making a difference."