“She created this mess and she knows it,” a close aide, Huma Abedin, wrote of Mrs. Clinton in a January 2015 email.
For months, the Clintons have defended their foundation, making public proclamations that it went above and beyond what the law required in terms of transparency while Mrs. Clinton was at the State Department.
The emails, which came from the account of John D. Podesta, who had a leadership role at the foundation and is now Mrs. Clinton’s campaign chairman, have not contained evidence to support Republican contentions that Mrs. Clinton performed any favors for foundation donors.
“Do they plan to do big events next year?” her campaign manager, Robby Mook, asked about the foundation last year, shortly after Mrs. Clinton kicked off her presidential campaign. “Possible for those to be smaller and lower key in 16?”
Founded in 1997, when Mr. Clinton was still president, the foundation has raised roughly $2 billion to fund projects around the world, helping African farmers improve their yields, Haitians recover from a devastating 2010 earthquake and millions of people gain access to cheaper H.I.V./AIDS medication, among other accomplishments.
Some of the former president’s staff members followed him from the White House to the foundation, and the emails provide an extraordinary look at the soap opera that unfolded years later as people close to the couple felt their power threatened.
“This is the 3rd time this week where she has gone to daddy to change a decision or interject herself,” Mr. Band, the longtime aide to Mr. Clinton, wrote about Chelsea Clinton in 2011.
At the time, she was beginning to exert influence at the foundation, expressing concerns that Mr. Band and others were trying to use the charity to make money for themselves, and accusing another aide in her father’s personal office of installing spyware.
Emails released on Tuesday contained a memo from Mr. Band essentially defending his work for the foundation, and for Mr. Clinton personally, even as Mr. Band was building up his political consulting firm, Teneo. The memo noted that some foundation donors had indeed been clients of Teneo, but also that Mr. Band and Teneo had helped raise tens of millions of dollars for the foundation from individual, foreign and corporate donors, without taking a commission.
Mr. Band also noted how some of those donors he had cultivated were paying Mr. Clinton privately to make speeches or to do other work. One such donor, Laureate International Universities, a for-profit education company based in Baltimore, was paying Mr. Clinton $3.5 million annually “to provide advice” and serve as its honorary chairman, Mr. Band wrote.In another email, Mr. Band wrote that Mr. Clinton had even received gifts from some donors.
The tensions came to a head when Chelsea Clinton helped enlist an outside law firm to audit the Clinton Foundation’s practices. Some interviewees told the audit team that the donors “may have an expectation of quid pro quo benefits in return for gift.” The audit suggested the foundation “ensure that all donors are properly vetted and that no inappropriate quid pro quos are offered to donors in return for contributions.”
The advice proved prescient as Mrs. Clinton faced intense scrutiny about whether donors to the Clinton Foundation had received special access to her State Department or other rewards. In August, the foundation said it would no longer accept foreign donations should Mrs. Clinton win the White House.
Mrs. Clinton has dismissed criticism of the charity as politically motivated. A spokesman for the Clinton campaign, Glen Caplin, declined to verify the authenticity of the emails, but said the hack was part of the Russian government’s efforts to use cyberattacks to influence the election in favor of the Republican nominee, Donald J. Trump.
Mr. Band’s firm released a statement saying: “Teneo worked to encourage clients, where appropriate, to support the Clinton Foundation because of the good work that it does around the world. It also clearly shows that Teneo never received any financial benefit or benefit of any kind from doing so.”
Behind the scenes, Mrs. Clinton’s aides grappled with how to sever her from the problematic optics of some of the philanthropy’s fund-raising practices.
In an October 2014 email, Mr. Mook asked whether Mrs. Clinton’s name would be used in connection with the foundation, which is formally known as the Bill, Hillary and Chelsea Clinton Foundation. “It will invite press scrutiny and she’ll be held accountable for what happens there,” he wrote.
The next year, when Mrs. Clinton was on the verge of declaring her candidacy, Cheryl D. Mills, a lawyer and top aide, said she discussed withMrs. Clinton various “steps” to take to adjust her relationship with the foundation, including her resignation from the foundation’s board.
By fall 2015, Mrs. Clinton’s aides had fine-tuned her response to questions about foreign donors. “As President, I won’t permit any conflicts between my work for the American people and the Foundation’s good work,” aides advised Mrs. Clinton to say in a coming debate.
The emails give insight into the periodic fires that Mrs. Clinton’s advisers thought they had to put out. Mrs. Clinton ultimately did not attend the foundation event in Morocco that Ms. Abedin had complained about; her husband and daughter did go. It is unclear if the king had given the $12 million he was said to have pledged; he is not listed among the foundation’s donors.
In March 2015, Victor Pinchuk, a Ukrainian steel magnate who had given more than $10 million to the foundation, was “relentlessly” requesting a meeting with Mr. Clinton, according to an aide, Amitabh Desai. If the former president declined, the relationship would be damaged, Mr. Desai wrote in an email.
“No is better. Is that viable?” wrote Mr. Podesta, who by then was the chairman of Mrs. Clinton’s campaign. It is unclear if the meeting took place.
That same year, during a discussion over a potential meeting between Mr. Clinton and the Saudi king, Mr. Podesta replied, using the former president’s initials, “Not something that would be on our top 10 list of WJC requests.”
Mr. Podesta took a leadership role at the charity when Bruce R. Lindsey, a former White House counsel and longtime friend of Mr. Clinton who had been chief executive of the foundation, had a stroke in 2011.
His role at the foundation, coupled with his later capacity as the chairman of Mrs. Clinton’s campaign, put Mr. Podesta in the middle of internal workings of both operations and, by default, the delicate battles unfolding between Chelsea Clinton and her father’s top aides.
The day Mrs. Clinton’s mother, Dorothy Rodham, died in 2011, Chelsea Clinton emailed Mr. Podesta. “Doug called and yelled and screamed at my Dad about how could he do this,” she said, a reference to the internal scrutiny going on at the foundation. “My mother is exhausted, we are all heartbroken but we need a strategy and my father needs advice/counsel.”
Mr. Band has said the exchange described in the email never happened.
Mr. Band, who helped Mr. Clinton build the foundation, clearly felt irritated by Chelsea Clinton’s stream of implications that he had padded his own pockets from his work for her father.“As they say, the apple doesn’t fall far,” he wrote. “A kiss on the cheek while she is sticking the knife in the back, and front.”
When Chelsea Clinton, using a pseudonym “Diane Reynolds,” that she also sometimes used to check into hotels, sent Mr. Band a complimentary email in January 2012, he forwarded it to Mr. Podesta and Ms. Mills.