Emails from Hillary Clinton’s home server contained information classified at levels higher than previously known, including a level meant to protect some of the most sensitive U.S. intelligence, according to a document obtained by NBC News.

In a letter to lawmakers, the intelligence community’s internal watchdog says some of Clinton’s emails contained information classified Top Secret/Special Access Program, a secrecy designation that includes some of the most closely held U.S. intelligence matters.

Two American intelligence officials tell NBC News these are not the same two emails from Clinton’s server that have long been reported as containing information deemed Top Secret.

The letter, first reported by Fox News, doesn't make clear whether Clinton sent or received the emails in question, but in the past, emails containing classified information have tended to have been sent to Clinton, not written by her.

The new revelation underscores the extent to which the email classification issue could continue to dog Clinton, as State Department and intelligence officials review sensitive information within messages that were blacked out before being released to the public.

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Clinton, who tops national primary polling as a Democratic presidential candidate, has repeatedly said that none of the information she sent or received while secretary of state was marked classified, and nothing has emerged to contradict that. But it’s become clear that classified information bled into the emails, which were sent over unencrypted channels open to interception by foreign intelligence agencies.

Charles McCulllough, the intelligence community’s inspector general, said in a letter to the chairmen of the Senate intelligence and foreign affairs committees that he has received sworn declarations from an intelligence agency he declined to name.

The declarations cover “several dozen emails containing classified information determined by the IC element to be at the CONFIDENTIAL, SECRET and TOP SECRET/SAP information.”

An intelligence official familiar with the matter told NBC News that the special access program in question was so sensitive that McCullough and some of his aides had to receive clearance to be read in on it before viewing the sworn declaration about the Clinton emails.

Clinton’s campaign did not immediately respond to a request for comment.

While she was secretary of state from 2009 to 2013, Clinton conducted government business over private email. The arrangement was particularly unusual because the email system relied not on Yahoo or Google but her own server, which she kept in her home in Westchester County, N.Y.

The State Department is under court order to release Clinton’s government-related emails under the Freedom of Information Act. Clinton has turned over about 55,000 emails, and almost all have been released, though they have been heavily censored. The last batch is due to be made public Jan. 29.

While Republicans have criticized Clinton over the issue, her defenders have pointed out that the State Department has long faced the problem of how to communicate about sensitive matters. Unlike the CIA, State does most of its business over an unclassified email system, and many officials do not have easy access to a classified messaging system.

State Department spokesman John Kirby said that the State Department is "focused on and committed to releasing former Secretary Clinton’s emails in a manner that protects sensitive information. No one takes this more seriously than we do. We have said repeatedly that we anticipate more upgrades throughout our release process. Our FOIA review process is still ongoing. Once that process is complete, if it is determined that information should be classified as Top Secret we will do so.”‎

-- Andrea Mitchell contributed reporting to this article.