The brief online video was not Nye's first foray into the combustible debate, but "it's the first time it's gotten to be such a big deal."
"I can see where one gets so caught up in this (debate) that you say something that will galvanize people in a bad way, that will make them hate you forever," he said. "But I emphasize that I'm not questioning someone's religion — much of that is how you were brought up."
In the video he tells adults they can dismiss evolution, "but don't make your kids do it. Because we need them." Posted by Big Think, an online knowledge forum, the clip went viral and has 4.6 million views on YouTube. It has garnered 182,000 comments from critics and supporters.
It drew the ire of the creationism group Answers in Genesis, which built a biblically based Creation Museum in Kentucky that teaches the stories of the Old Testament and has attracted headlines for its assertion that dinosaurs roamed alongside Adam and Eve.
The group produced a response video featuring two scientists who say the Bible has the true account of Earth's origins, and that "children should be exposed to both ideas concerning our past."
Nye, who is prone to inject dry humor into scientific discussions, said Earth is about 4.5 billion years old.
"What I find troubling, when you listen to these people ... once in a while I get the impression that they're not kidding," Nye said.
Ken Ham, a co-founder of Answers in Genesis, said dating methods used by scientists to measure the age of the earth are contradictory and many don't point to millions or billions of years of time.
"We say the only dating method that is absolute is the Word of God," Ham said. "Time is the crucial factor for Bill Nye. Without the time of millions of years, you can't postulate evolution change."
America is home to the world's biggest creationist following, Ham said, and the $27 million Creation Museum has averaged about 330,000 visitors a year since it opened just south of Cincinnati in 2007.