By Jonathan Allen

NEW YORK (Reuters) - Two aides in charge of running Hillary Clinton's presidential campaign were taken aback as news broke in March 2015 of Clinton's use of private email for her work as U.S. secretary of state, according to stolen emails published on Thursday by WikiLeaks.

The late-night exchange between Robby Mook, Clinton's campaign manager, and John Podesta, the campaign chairman, happened within hours of the New York Times breaking the news that Clinton exclusively used a private email account in a way that may have broken records rules.

"Did you have any idea of the depth of this story?" Podesta wrote to Mook at 10:27 p.m. on the night the Times story appeared online, according to an exchange published by WikiLeaks.

A few hours later, at 1:32 a.m., Mook wrote back: "Nope. We brought up the existence of emails in research this summer but were told that everything was taken care of."

The exchange took place hours before the Associated Press reported for the first time the following morning that Clinton's email system was run off a private server Clinton kept in the basement of her home in Chappaqua, New York.

The exchange appears to show that even Clinton's most senior aides were initially unprepared for the scale of revelations about Clinton's email practices, which would end up dogging her campaign all the way through to the final weeks leading up to the Nov. 8 election. Clinton, the Democratic candidate, remains the front-runner in opinion polls over Republican opponent Donald Trump.

Many voters have pointed to the unauthorized email system, which stymied attempts by the public to seek Clinton's emails through open-records laws, as a reason they find Clinton untrustworthy. Trump has repeatedly attacked her over her emails, saying Clinton should be in prison because she sent and received classified government secrets through the server.

After a yearlong investigation, James Comey, the director of the Federal Bureau of Investigation, said in July that Clinton and her staff were "extremely careless" with classified information, but that no reasonable prosecutor would bring charges.

The same night of the Mook-Podesta exchange, Neera Tanden, a longtime Clinton confidante, wrote to Podesta to express her frustration, according to other emails stolen from Podesta's account and published in daily batches this month by WikiLeaks, a publishing organization that advocates extreme government transparency.

"Why didn't they get this stuff out like 18 months ago?" Tanden wrote, criticizing Cheryl Mills, a lawyer working for Clinton and Clinton's former chief of staff at the State Department. "So crazy."

Podesta replied with a single word: "Unbelievable."

"I guess I know the answer," Tanden, an outside adviser who does not have a formal role in the campaign, responded. "They wanted to get away with it."

Podesta also suggests in the exchange that other Clinton aides withheld information about the emails, although it is unclear if he meant from the public or other colleagues.

"Speaking of transparency, our friends Kendall, Cheryl and Phillipe sure weren't forthcoming on the facts here," Podesta wrote. David Kendall is another lawyer working for Clinton, and Philippe Reines, whose first name Podesta appeared to have misspelled, is a Clinton adviser who handled her news coverage at the State Department.

Tanden did not respond to questions.

Glen Caplin, a Clinton campaign spokesman, declined to comment on the exchanges, saying the campaign was not confirming the authenticity of the emails. It has not pointed to any instances of doctored messages. He criticized Trump for supporting WikiLeaks, which Caplin said was "weaponizing" the emails he said were hacked by the Russian government.

"Every American, regardless of party, should be concerned by this national security issue," he said in a statement. Sergei Lavrov, Russia's foreign minister, said this month the accusation his government is behind a spate this year of stolen emails from Democratic Party operatives was "flattering" but without proof.

Nearly five months after the news of Clinton's private email first broke, Tanden again wrote to Podesta to link the arrangement to unfavorable public polling that week.

"Do we actually know who told Hillary she could use a private email?" she wrote. "And has that person been drawn and quartered?"

(Editing by Jonathan Oatis)