"We must not witness or permit such hate and bigotry in our country, and we must be unequivocal about it," Cook said in the email.
"I disagree with the president and others who believe that there is a moral equivalence between white supremacists and Nazis, and those who oppose them by standing up for human rights. Equating the two runs counter to our ideals as Americans."
He said this position was not a matter of politics, but about "human decency and morality."
In light of Charlottesville, Cook said Apple will donate $1 million each to the Anti-Defamation League and the Southern Poverty Law Center - organizations that track hate groups.
The company will also match "two-for-one" employee donations to these and other human rights groups through the end of September, the email said.
"In an email to employees, Apple CEO Tim Cook announces that the company is donating US$1 million (NZ$1.7m) each to the ADL and SPLC.
- Yashar Ali (@yashar) August 17, 2017"
"We've seen the terror of white supremacy & racist violence before. It's a moral issue - an affront to America. We must all stand against it
- Tim Cook (@tim_cook) August 14, 2017"
"Heartbreaking scenes in #Charlottesville. Violence and racism have no place in America.
- Tim Cook (@tim_cook) August 12, 2017"