State Department spokesman John Kirby said the emails, which he described as "22 documents covering 37 pages" from seven email chains during Clinton's tenure as secretary of state, would therefore not be released publicly.
Republicans debate without Trump, who taunts from afar
Another 18 emails, from eight email chains, sent between then secretary Clinton and President Barack Obama will also not be released. But Kirby said those exchanges did not contain classified information.
Although emails previously released by the State Department have been partially redacted due to the nature of the information they contained, this was the first time entire messages were withheld.
The revelation about the top secret emails comes three days before Clinton - the frontrunner for the Democratic presidential nomination - goes to battle in the Iowa caucus, the first time the public will cast ballots on the long road to Election Day in November.
"These documents were not marked classified at the time they were sent," Kirby told a news briefing, explaining that the emails had been reviewed prior to public release and found to contain top secret information.
"The documents are being upgraded at the request" of US intelligence agencies.
Senator Dianne Feinstein, the vice chair of the Senate Intelligence Committee, said that "none" of the email chains originated with Clinton or contained the mandatory markings that are required to accompany classified information when shared.
She described the material as being contained in 22 separate emails.
"The only reason to hold secretary Clinton responsible for emails that didn't originate with her is for political points, and that's what we've seen over the past several months," Feinstein added.
Hillary responds to question on Islamophobia with severe criticism of Trump
Clinton's campaign reacted with fury to the announcement, demanding that the emails be released in full, to defuse a burgeoning scandal that could critically damage her 2016 presidential hopes.
Campaign spokesman Brian Fallon said the review process "appears to be over-classification run amok."
"We understand that these emails were likely originated on the State Department's unclassified system before they were ever shared with Secretary Clinton, and they have remained on the department's unclassified system for years," he said.
Kirby said the State Department was separately investigating whether those emails should have been marked classified at the time. The FBI is also probing Clinton's use of a private email server.
The disclosures triggered fresh Republican attacks on Clinton.
"If someone on my staff did what she did, you know what would happen? They would be fired and they would be prosecuted," said Senator Marco Rubio.
"She is disqualified just because of that."
Republican National Committee Chairman Reince Priebus said that with the latest revelations, "Hillary Clinton has removed all doubt that she cannot be trusted with the presidency."
He said her use of a private server "put our national security and diplomatic efforts at risk."
Rival Democrat Bernie Sanders, however, called for the legal process reviewing the emails to "not be politicized."
In a memorable campaign line, he said during an October presidential debate as he turned to face Clinton: "The American people are sick and tired of hearing about your damn emails."
Clinton's successor as US Secretary of State, John Kerry, refused to be drawn on the widening scandal and whether the use of a private server to send the emails had threatened national security.
"I can't speak to the specifics of anything with regard to the technicalities, the contents, what may or may not have taken place with respect to her personal server because that's not our job. We don't do that," he told reporters.
"We don't know about it. It's in other hands," Kerry said, explaining that the State Department's responsibility was to release the mails according to the court order and not to comment on their contents.
In the buildup to the scheduled late Friday document dump, several leaks to US media had suggested that highly secret information had been found on Clinton's private server, which she used while in office instead of an official government account.
The revelation of the so-called "homebrew" server was an early embarrassment for her campaign, but she has long insisted that no information marked as classified had been put at risk by her unusual arrangement.
Her campaign returned to this theme in her statement.
"After a process that has been dominated by bureaucratic in-fighting that has too often played out in public view, the loudest and leakiest participants in this interagency dispute have now prevailed in blocking any release of these emails," it said.
"This flies in the face of the fact that these emails were unmarked at the time they were sent, and have been called 'innocuous' by certain intelligence officials."
PHOTO: REUTERS
DES MOINES, UNITED STATES: Republican White House hopefuls emboldened by the absence of frontrunner Donald Trump jostled for the limelight at their final debate before the nomination votes begin, as the billionaire disrupted the showdown with his own controversial event.
Trump gambled big when he announced he was boycotting the debate because of a feud with Fox News over alleged bias against him, plunging the presidential race into uncharted waters just days before Iowans vote February 1.
To some Republicans, Trump gives voice to what’s on their minds
The real estate mogul doubled down, in a game of political chicken, scheduling a rival event for military veterans at the same time as his party showcases its candidates to Iowa voters.
Straight out of the gate the seven debaters turned to the elephant-not-in-the-room, with top adversary Ted Cruz using Trump-like language to humorously belittle himself and rivals.
“I’m a maniac and everyone on this stage is stupid, fat and ugly. And Ben, you’re a terrible surgeon,” Cruz said, looking mischievously at retired neurosurgeon Ben Carson.
“We’ve gotten the Donald Trump portion out of the way,” he quipped.
All eyes are on the heartland state of Iowa, where 12 Republican candidates and three Democratic hopefuls including Hillary Clinton are vying for both bragging rights and momentum as the primary race heads next to New Hampshire, South Carolina and Nevada.
Trump had taunted Fox and his rivals, saying the debate would be a “total disaster” with low ratings.
On Trump, Islamophobia and hate speech
The tycoon took the stage at his own event, just a few miles from his rivals, about 15 minutes after the debate began.
“I said I’m not going to do the debate out of respect for myself,” he said to cheers from the overflow crowd.
“But I love Iowa. I’m here.”
Adding to the spectacle, rival Mike Huckabee, the former Arkansas governor who is languishing in polls and attended an undercard event before the main debate, joined Trump at his veterans event, as did low-polling former senator Rick Santorum.
With Trump out of the way, Cruz and fellow Republicans launched into spirited debate about foreign policy and tackling the militant threat.
“I believe only with a strong America will we defeat this radical group called IS,” said Senator Marco Rubio, running third in national polls.
“If we capture any of these IS killers alive, they are going to Guantanamo Bay, Cuba.”
Donald Trump calls for barring Muslims from entering US
Senator Cruz defended himself when asked about a controversial call for “carpet-bombing” Islamic State group fighters, while not voting for President Barack Obama’s defense authorization request three years in a row.
“You claim it is tough talk to discuss carpet-bombing. It is not tough talk, it is a different fundamental military strategy than what we’ve seen from Barack Obama,” he said.
But even off the main stage, Trump’s shadow loomed large over the evening — and he was snatching many of the headlines.
Analysts have been riveted by the unexpected drama and disruption to the typical Iowa political playbook. The last major candidate to skip a pre-Iowa caucus debate was Ronald Reagan, in 1980.
“Wow. What a chess game,” Iowa State University political science professor Steffen Schmidt declared of the political theater.
Trump has accused Fox News, and especially debate moderator Megyn Kelly, of bias against him.
Shortly before the debate he told CNN that top Fox officials called him to apologise. Trump said he was mulling a last-minute appearance at the debate, but then his veterans event “took on a life of its own” and he felt compelled to appear there instead of the debate.
Presidential hopeful Trump blasts Republican expected to endorse rival
Trump has a genuine battle on his hands in Iowa with ultra-conservative Cruz who trails by about five percentage points in the RealClearPolitics average of recent Iowa polls.
Cruz, who has earned endorsements from key evangelicals and anti-abortion figures who tout his conservative and religious values, insists the race is winnable.
His team claims its ground game is second to none in Iowa, with 12,000 volunteers and staff blanketing the state.
Nationally, Trump keeps soaring. A recent CNN/ORC poll of Republican voters has Trump at 41 per cent to 19 per cent for Cruz, with more than two-thirds of Republicans saying they believe the billionaire developer will be the party’s presidential candidate.
Early Thursday, Cruz told Fox it was “stunning” that Trump refused to debate, challenging him to a one-on-one showdown.
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