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CAMBRIDGE, Mass. — Harvard University and its president on Monday made their first public comments on the university’s searching of staff members’ email accounts, and offered a qualified apology for keeping the searches secret from most of the employees involved.

The episode has angered faculty members and refocused attention on Harvard’s largest cheating scandal in memory, which involved a take-home final exam in a government class last spring. After an investigation, about 70 students were forced to take a leave of absence.

In September, when confidential information about cheating cases appeared in news reports, administrators ordered searches of the email accounts of 16 resident deans, to find the source of the leaks.

In an online statement posted Monday morning, university officials acknowledged the searches and explained their reasoning. The statement eased the concerns of some faculty members but did not alleviate them completely, and professors said they expected that email privacy would be the topic of a full-throated discussion at the next faculty meeting, in early April.

In her first comment on the matter, Harvard’s president, Drew Gilpin Faust, said that she did not know about the searches at the time, but that having been apprised, “I feel very comfortable that great care was taken to safeguard the privacy of all concerned.”

Faculty responses revealed a gap between expectations in academia, where privacy is often seen as integral to academic freedom, and the corporate world, in which employees are often told to assume that workplace emails are not private. Some professors wondered aloud whether they had been naïve to think that things would be different at a university, and said they were forced to re-examine assumptions about confidentiality.

“It’s disturbing because I don’t know what it means about whether they could look at my own email,” said Oliver Hart, an economics professor. “We need to have a discussion and a better understanding of the policy.”

He and other professors said the searches would prompt them to conduct more business through private email accounts outside of Harvard’s reach.

Most professors who agreed to discuss the matter on Monday insisted on anonymity, not wanting to run afoul of the administration. Several of them, conceding that the university had a legal right to conduct the searches, said the problem was, as one put it, that “we never thought they would — we never thought about it at all, and we probably should have.”

One leak last year involved an email from the university’s Administrative Board to resident deans, offering guidance on how to advise students accused of cheating. Some have questioned why such a minor breach prompted an investigation.

But the statement posted Monday, attributed to Michael D. Smith, dean of the faculty of arts and sciences, and Evelynn M. Hammonds, dean of Harvard College, said administrators were more troubled by another leak, recounting closed-door discussions by the Administrative Board.

“The disclosure of the document and nearly word-for-word disclosure of a confidential board conversation led to concerns that other information — especially student information we have a duty to protect as private — was at risk,” the deans wrote.

Resident deans live among students in Harvard’s residential houses and act as student advisers, and they are also lecturers, meaning that they teach courses but are not on a tenure track to professorship. Each one generally has a personal Harvard email account and one specifically for the job of resident dean.

The deans’ statement on Monday emphasized that the search was conducted only of the resident dean accounts, not personal ones, and only for the subject line on each message, to determine whether the confidential email had been forwarded.

The search determined that one resident dean had forwarded the email to two students who were accused of cheating and had sought the dean’s advice.

Hammonds and Smith wrote that the resident dean who had forwarded the messages did so in good faith and was not punished. The statement did not say whether administrators determined how the email found its way to the news media, or who was responsible for the other leak, of the Administrative Board’s deliberations.

That resident dean and one other were told about the email searches shortly after they took place, administrators said, but the other 14 resident deans were not told until last week, after The Boston Globe inquired about the matter.

They were not told to protect “the privacy of the resident dean who had made an inadvertent error,” Hammonds and Smith wrote. “We understand that others may see the situation differently, and we apologize if any resident deans feel our communication at the conclusion of the investigation was insufficient.”

On his blog, Michael Mitzenmacher, a computer science professor, wrote that he was satisfied with some parts of the administration’s explanation, but “in my opinion, the administration made an error in judgment” in not telling the resident deans of the search.

Wilfried Schmid, a mathematics professor, said he still wanted to know more about what happened. “I certainly get the sense that many of my colleagues will be upset, and so there will be a discussion,” he said.

But he urged the faculty not to lose sight of what he considered the bigger issue, the cheating episode itself.