Jack Hawkins, chancellor of Troy University, sent a New Year's video message to all students and staff saying the freedom of Americans would be under threat if people didn't go back to church.
The video, narrated by Clayton Christensen, explained how the falling number of people going to church could be to blame for the increase in crime and moral decay in society.
"What will happen to our democracy? Where are the institutions that are going to teach the next generation of Americans that they too need to voluntarily obey the laws?" the video asked.
"Because if you take away religion, you can't hire enough police," it added.
Atheist groups are now demanding an apology from the university head for the "anti-patriotic sentiment".
American Atheists said in a statement: "We demand an apology from you for using the public university email system and your publicly funded position to disparage atheists and minority religious groups as well as perpetuating the discrimination and anti-patriotic sentiment against atheists in the United States."
"In fact, in the United States, in states with the highest percentages of atheists, the murder rate is lower than average. In the most-religious states, the murder rate is higher than average," it said.