Law enforcement officials have said that the emails were discovered by agents investigating whether former Congressman Anthony Weiner, using devices including a laptop computer, sent illicit messages and photos to an underage girl. The agents found that Weiner's wife, current and former top Clinton aide Huma Abedin, used the same laptop to send thousands of e-mails to Hillary Clinton.
The officials familiar with the discussions said while the Justice Department did not prohibit the FBI, which is a DOJ agency, from sending the letter, it strongly advised against it.
They cited long-standing policies against disclosing details of investigations that are underway or taking actions that could affect an election, especially in the period leading up to one.
That was especially so, they said, given that FBI agents have not yet analyzed the newly discovered e-mails to see if they contain classified information, the central issue in the investigation of the Clinton private e-mail server.
Comey's letter said the FBI learned "of the existence of e-mails that appear to be pertinent" to the Clinton investigation, though he added that the FBI "cannot yet assess whether or not this material may be significant."
In an internal note sent to FBI employees, Comey said "we don't ordinarily tell Congress about ongoing investigations, but here I feel an obligation to do so given that I testified repeatedly in recent months that our investigation was completed."
"I also think it would be misleading to the American people were we not to supplement the record. At the same time, however, given that we don't know the significance of this newly discovered collection of e-mails, I don't want to create a misleading impression," his note said.
"We were well aware of the policies DOJ was citing," the FBI official said Saturday, "and we all understood them."
But the official said the FBI also believed it was highly probable that word of the development would leak, "and be translated through all kinds of different forums, which would be worse."