"It would be misleading to the American people were we not to supplement the record," Comey wrote in the letter published by the Washington Post.
He acknowledged the possibility of creating a "misleading impression," particularly given the proximity to Election Day, but wrote that he felt an "obligation" to inform Congress.
"In trying to strike that balance, in a brief letter and in the middle of an election season, there is significant risk of being misunderstood," Comey wrote.
In a letter sent to lawmakers early Friday afternoon, Comey wrote that his agency was looking into emails "pertinent" to the FBI's previous investigation into Clinton's use of a private server as secretary of state.
Republicans were quick to jump on the news and criticize Clinton, while the Democratic nominee's campaign called on the FBI to provide "full details" about the emails in question.
Read the full letter from Comey below:
This morning I sent a letter to Congress in connection with the Secretary Clinton email investigation. Yesterday, the investigative team briefed me on their recommendation with respect to seeking access to emails that have recently been found in an unrelated case. Because those emails appear to be pertinent to our investigation, I agreed that we should take appropriate steps to obtain and review them.
Of course, 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 emails, I don’t want to create a misleading impression. In trying to strike that balance, in a brief letter and in the middle of an election season, there is significant risk of being misunderstood, but I wanted you to hear directly from me about it.