Fang Binxing was lecturing at Wuhan University, Hubei province, when the alleged protest took place.
Reports of the attack spread quickly on Twitter after a user named Hanunyi posted his account of the incident.
Mr Fang is reviled by many Chinese web users for overseeing development of China's system of internet censorship.
The computer scientist, who is Principal of Beijing University of Posts and Telecommunications, has been dubbed the Father of the Great Firewall.An officer at Luojiashan Public Security Bureau confirmed police were investigating the alleged attack, AP news agency reported.
Hanunyi posted a live account of the alleged shoe-throw on his profile page, including a picture of a hand clutching an egg.
"The egg missed the target. The first shoe hit the target. The second shoe was blocked by a man and a woman," he tweeted. (read more)