"As the CEO of Merck, and in my soul and conscience, I consider it my responsibility to take a stand against intolerance and extremism", said Mr. Frazier, 62, the CEO of Merck since 2011.
He was nearly immediately attacked by Trump on Twitter.
After neo-Nazis and white supremacists brawled with counter-protesters in the streets of Charlottesville on Saturday, Trump spoke against violence "on many sides - on many sides".
Kenneth Frazier, the CEO of the giant american of the pharmacy of Merck, announced on Monday that he would resign from his duties as economic adviser to Donald Trump to protest against the declarations of the latter after the violence of Charlottesville.
The tweet is sure to prompt critics to pounce on Trump for being Trump. By then nearly two days had passed since the president's first remarks on Charlottesville - and some of the nation's most prominent business leaders had filled the gap with denunciations of racism. "#Intel asks all our countries leadership to do the same", CEO Brian Krzanich said in a tweet.
Tesla and SpaceX CEO Elon Musk left the group earlier this year after Trump pulled out of the Paris climate agreement.
On Monday, Trump finally condemned white supremacists, saying, "Racism is evil - and those who cause violence in its name are criminals and thugs, including KKK, Neo-Nazis, white supremacists, and other hate groups are repugnant to everything we hold dear as Americans".
Trump said on Twitter that he has other CEOs ready to step in and that "grandstanders" should not have joined the manufacturing council in the first place.
Frazier's message was clear: "America's leaders must honor our fundamental values by clearly rejecting expressions of hatred, bigotry and group supremacy". "I'm thankful we have business leaders such as Ken to remind America of its better angels", said Hewlett Packard Enterprises CEO Meg Whitman, who ran for governor of California as a Republican in 2010.
I wish I could tell why just by looking at them. "It's absolutely critical that they use that platform". "He knows only one mode: When attacked, hit back harder". The organization is chaired by JPMorgan CEO Jamie Dimon.
The industry's silence comes as Trump is finalizing an executive order on drug prices that would relax industry regulation and contains measures that, some say, would protect existing drug prices or even increase them.
It's a stunning reversal considering the euphoria among business leaders following Trump's election.
The AFL-CIO, a federation of labor unions that represent 12.5 million workers, said it was considering pulling its representative on the committee.
Wall Street seemed unfazed by Trump's attack.
The AFL-CIO, which has two members on the council, said Monday that it denounces "bigoted domestic terrorists" and called on Trump to follow.
At the same time, CEOs have become frustrated with Trump's inability to get his tax, infrastructure, health care or deregulation plans through Congress.
Former Uber Technologies Inc CEO Travis Kalanick quit the business advisory council in February amid pressure from activists and employees who opposed the administration's immigration policies.