The scholar has been criticised by the authorities and lawmakers after he defended those mourning a man who died after stabbing a policeman on the July 1 handover anniversary.
Chan said people could simply be mourning out of sympathy or to show their discontent with the government.
Lee refused to say whether his “sinners” remark was aimed specifically at Chan, or whether the professor could be prosecuted.
He said only that people with a legal background should know that their words have an impact on society, and everyone has to bear legal and moral responsibilities for comments they make.
“It is important that everybody who says something knows that there may be a consequence, particularly for the extremists who may have been already embedded with some extreme ideas,” Lee said.
“If there is any indication that may suggest to him that his sin can be exonerated simply because of what he believes, that is a very dangerous thing.”
On Tuesday, Security Secretary Chris Tang warned that people who show sympathy for terrorists will turn into terrorists themselves.