Hillary Clinton is vehemently disputing new charges that she sent top-secret information from a nonsecure email account while at the State Department, but analysts say the scandal has already damaged her so deeply that her presidential ambitions are at risk.

Mrs. Clinton’s messages contained some information classified above “top secret,” the intelligence community’s inspector general said in a letter to Congress this week. Fox News reported Thursday that the information is so sensitive that even senators, who already have clearance, must go through additional hoops if they want to see some of what she was sending.

The Clinton campaign responded by accusing the inspector general, I. Charles McCullough, appointed by President Obama, of politically motivated leaks to sabotage her campaign.

But she is suffering from the slow drip of the email scandal. Surveys show voters see her chief primary challenger, Sen. Bernard Sanders, as much more honest and trustworthy.

“Trustworthiness is not a problem by itself for Clinton, but combined with other past and present scandals weighing her down, alternative candidates like Sanders begin to look more appealing,” said Brandon Rottinghaus, a political science professor at the University of Houston who specializes in political leadership. “For a candidate with enough negative stories and rumors about them as Hillary Clinton, her campaign can refute individual charges to win a daily news battle but lose the larger perception war.”

There is ample evidence that the war already has been lost.

A recent Quinnipiac University Poll found that 93 percent of Democratic primary voters consider Mr. Sanders honest and trustworthy, while just 66 percent said the same of Mrs. Clinton.

A CNN survey conducted this month found that 55 percent of Democratic voters consider Mrs. Clinton to be the “least honest” candidate in the race.

Against that backdrop, reports surfaced this week that Mrs. Clinton’s private email server contained several dozen more classified emails than previously thought, including some from “special access programs,” or SAP.

Even top members of the Senate Committee on Foreign Relations are unable to view such messages without additional security steps, including signing new nondisclosure agreements, Fox News reported.

“These declarations cover several dozen emails containing classified information determined to be at the confidential, secret and top secret/sap levels,” Mr. McCullough said in a letter to lawmakers obtained by The Associated Press.

Mrs. Clinton pushed back against the reports in an interview with NPR Wednesday, sticking to the story that she never knowingly sent or received classified email on her private server, which was housed outside the formal State.gov domain.

“As the State Department has confirmed, I never sent or received any material marked classified, and that hasn’t changed in all of these months,” she said, blaming congressional Republicans for the continued focus on her emails. “This seems to me to be, you know, another effort to inject this into the campaign. It’s another leak.”

Her campaign argued that the emails appear to have been forwards of a New York Times article on a classified drone program, and say the messages seem to have been retroactively classified.

“How a New York Times public article that goes around the world could be in any way viewed as classified, or the fact that it would be sent to other people off of The New York Times site, I think, is one of the difficulties that people have in understanding what this is about,” Mrs. Clinton told NPR.

The State Department is under a court order to produce about 55,000 emails from Mrs. Clinton’s home server. Most have been released, with the last of them expected on Jan. 29 — just days before the Iowa caucuses on Feb. 1.

Mrs. Clinton’s use of private email has dogged her since it was first revealed publicly in March 2015. She began returning her emails to the State Department after the Obama administration, prodded by a House investigation into the Benghazi affair, discovered Mrs. Clinton had taken all of her messages with her when she left the State Department at the end of Mr. Obama’s first term.

The administration then said that Mrs. Clinton had refused to use a regular email account on the State.gov email server and instead used a private server that she kept in her home in New York.

Mrs. Clinton has since said she regrets using the private server, but has steadfastly maintained that she did not use the private account to send or receive classified information.

Investigations also have found that the State Department routinely has botched open records requests for Mrs. Clinton’s emails. As of Jan. 7, 177 requests for documents from Mrs. Clinton were still pending, according to the State Department inspector general.

Specialists say that voters on the fence in the Democratic primary election may very well take the email scandal — and the larger questions about Mrs. Clinton’s honesty — into account when picking a candidate.

“The problem for Hillary Clinton is that there are alternatives to her candidacy in Bernie Sanders. This is why polls of Democrats don’t think Sanders can win [the general election] but are willing to vote for him anyway,” Mr. Rottinghaus said.

• This story is based in part on wire service reports.

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