Kenneth Frazier of Merck said in a statement: "America's leaders must honor our fundamental values by clearly rejecting expressions of hatred, bigotry and group supremacy."

Within minutes, Trump attacked him on Twitter, saying Frazier's resignation will give him "more time to LOWER RIPOFF DRUG PRICES!"

Frazier did not mention the violence in Charlottesville, Virginia, in his statement, but he did say that "as a matter of personal conscience, I feel a responsibility to take a stand against intolerance and extremism."

That appeared to be a reference to Trump's statement over the weekend blaming violence "on many sides" after neo-Nazis and white nationalists clashed with counter-protesters.

Frazier is one of the country's most prominent black corporate executives and was the only black male CEO named to the council in January.

His exit marks another rebuke to Trump from corporate America. Trump's June 1 decision to leave the Paris climate accord led Tesla (TSLA) CEO Elon Musk to step down from the manufacturing panel as well as a separate business advisory council.

Frazier appeared at the White House just last month to promote an agreement between Merck, Pfizer (PFE) and Corning (GLW) to create 1,000 jobs.

Trump formed the manufacturing council a week after his inauguration as part of a push to create jobs. At the time, the White House hailed the council, including Frazier, as "some of the world's most successful and creative business leaders."

At the group's first meeting in January, Trump shook Frazier's hand after the CEO talked up efforts to bring manufacturing jobs back to the U.S. for a cancer drug.

"That's very good," Trump said at the time.

--CNNMoney's Patrick Gillespie contributed to this report.