Emails concerning the Benghazi attacks and correspondence with general David Petraeus were not sent where they should have been and are being handed over

Just days after saying that she had provided all her emails to authorities investigating Hillary Clinton’s use of a private server, it has emerged that two tranches of the democratic presidential candidate’s emails were not sent where they should have been.

The Daily Beast reported on Friday that the State Department had failed to provide a “small number” of emails to a select congressional committee investigating the 2012 attack on a US diplomatic compound in Benghazi, Libya.

They are being handed over as part of 925 new documents the department is giving the committee, which a State Department spokesperson told the Guardian was partly because the committee was widening its scope from the attack in September 2012 to the civil war in Libya at large. “The documents provided today do not alter the fundamental facts known about the Benghazi attacks,” the official said.

Separately, the Obama administration announced on Friday that it, too, had discovered a new chain of emails that Clinton had failed to turn over, these between Clinton and general David Petraeus, who was chief of the military’s central command – Centcom – at the time.

Asked by the Guardian, the State Department official said he did not know “how or why” the administration had failed to turn the Petraeus emails over originally as part of the 55,000 emails which Clinton had previously said were the full record of her work-related correspondence as secretary of state.

The messages were exchanged with Petraeus when he headed Centcom, responsible for running the wars in Iraq and Afghanistan, officials said.

They began before Clinton entered office and continued into her first days at the State Department. They largely pertained to personnel matters and don’t appear to deal with highly classified material, officials said, but their existence further challenges Clinton’s claim that she has handed over the entirety of her work emails from the account.

She initially described the private server as a matter of convenience, but later took responsibility for making a wrong decision. Since then, she has denied wrongdoing. “When I did it, it was allowed, it was above board. And now I’m being as transparent as possible, more than anybody else ever has been,” she said earlier this week.

The revelations could not come at a worse time for Clinton, who has been dogged for months by questions about her email practices.

Her poll numbers have also been slipping in recent weeks. The latest poll of likely Democratic primary voters in New Hampshire show the former secretary of state 16 points behind the frontrunner, Vermont senator Bernie Sanders.

Her favorability rating has dropped six points since last March, and a Fox News national poll this week found 58% of responders believed she had lied about how her emails were handled while secretary of state.

The House Benghazi Committee plans to hold a public hearing with Clinton next month to hear specifically about what the emails might say about the attack on a US diplomatic outpost in Libya that killed four Americans on 11 September 2012.

And the Senate Judiciary Committee’s GOP chairman said he wants the Justice Department to tell him if a criminal investigation is underway into Clinton’s use of private email amid reports this week that the FBI recovered deleted emails from her server. The Senate Homeland Security Committee also is looking into the matter.

The senior State Department official told the Guardian that the Benghazi emails included “a few that were missed in the initial hand-review done in paper form early this year as well as some that were substantially personal in nature but reference Benghazi”. He said that none of them “alter the fundamental facts known about the Benghazi attacks”.

The Petraeus emails, however, represent a more serious breach of protocol. The State Department’s record of Clinton emails begins on 18 March 2009 – almost two months after she entered office. Before then, Clinton has claimed, she used an old AT&T Blackberry email account, the contents of which she no longer can access.

The Petraeus emails, first discovered by the Defense Department and then passed to the State Department’s inspector general, challenge that claim. They start on 10 January 2009, with Clinton using the older email account. But by 28 January – a week after her swearing in – she switched to using the private email address on a homebrew server that she would rely on for the rest of her tenure. There are fewer than 10 emails back and forth in total, officials said, and the chain ends on 1 February.

The officials who first spoke about the Petraeus emails weren’t authorized to speak on the matter and demanded anonymity. But State Department spokesman John Kirby confirmed that the agency received the emails in the “last several days” and that they “were not previously in the possession of the department”.

Kirby said they would be subject to a Freedom of Information Act review like the rest of Clinton’s emails. She gave the department some 55,000 emails last year that she sent or received while in office, and officials plan to finish releasing all of them by the end of January, after sensitive or classified information is censored.

Additionally, Kirby said the agency will incorporate the newly discovered emails into a review of record retention practices that Clinton’s successor, Secretary of State John Kerry, initiated in March. “We have also informed Congress of this matter,” he added.

Jamal Ware, the communications director for the Benghazi investigation select committee, said in a statement that it had been the committee’s requests that led the State Department to realize that it had not provided the Benghazi emails.

Ware said in his statement that the production of the new set of emails from the State Department – described as a “handful” by the State Department official – were a sign that relations between the committee and the department might be improving.

“The State Department, which has failed to comply with multiple Benghazi Committee requests and failed to act in good faith, is now indicating it intends to foster a more cooperative relationship with the committee,” he said. “It’s curious the Department is suddenly able to be more productive after recent staff changes involving those responsible for document production.”

The committee has not yet received the emails, Ware continued, and will not be issuing any statements about them until they can be “thoroughly examined”.

“If indeed this is a sign the stonewalling and political protection effort that was previously being run by the Department is diminishing, the Committee welcomes it,” Ware said. “The proof will be in the production.”