By the end of the day, though, the group’s leaders were no longer able to contain the damage.

Jennifer Fearing, who worked as a lobbyist for the Humane Society, said early Friday that because of the board’s decision to retain Mr. Pacelle, she would not renew her contract to work for the organization.

“I can’t make any sense of the board’s decision to end the investigation,” she said. “Women were still coming forward yesterday. That these so-called leaders weren’t inclined to learn more about the sexualized culture that many employees experienced over many years is beyond comprehension to me and feels like a betrayal of trust.”

As chief executive, Mr. Pacelle expanded the organization’s focus beyond the protection of cats and dogs to efforts like opposing puppy mills, dogfighting, abuse of seals and some industrial farming practices.

Through a series of mergers, affiliations and corporate partnerships with other animal protection and animal care groups, Mr. Pacelle, who held his position since 2004, is credited with building the Humane Society into the nation’s 138th largest charity. The organization had more than $210 million in net assets at the end of 2016, according to its latest nonprofit filings. Records put Mr. Pacelle’s base salary at more than $330,000 in 2016.

Explaining the board’s decision to retain Mr. Pacelle after an hours-long telephone meeting, one board member, Erika Brunson, 83, said in an interview that she was aware only of what she called a “ridiculous” old accusation against him regarding an alleged affair.

She said Mr. Pacelle had “done nothing wrong.”

“Which red-blooded male hasn’t sexually harassed somebody?” she added. “Women should be able to take care of themselves.” On Friday, Ms. Brunson resigned from the board.

But some people who worked with Mr. Pacelle said they believed the board had erred by not firing him.