Obama appeared to be critical of FBI director James B Comey in his remarks even as the White House refuted suggestions that the president gave any such impression.
"I do think that there is a norm that, you know, when there are investigations, we don't operate on innuendo. We don't operate on incomplete information. We don't operate on leaks.
Comey had said the emails may or may not be pertinent to an earlier investigation into Democratic presidential nominee Clinton's handling of classified information.
Obama said he has made a "very deliberate effort to make sure that I don't look like I'm meddling" in what are supposed to be independent processes for making these assessments as he went on to make his veiled criticism of Comey's handling of the issue without naming him.
"When this was investigated thoroughly the last time, the conclusion of the FBI, the conclusion of the Justice Department, the conclusion of repeated congressional investigations was that she had made some mistakes but that there wasn't anything there that was prosecutable," he said.
Democrats have questioned the agency's motive behind its decision taken days before the November 8 election, and Clinton and her campaign have pressed Comey to put out the "full and complete facts" about the probe.
"Nothing changed. If you read the full transcript of the President's remarks, you will see that the President went out of his way that he wasn't going to comment on any specific investigation. The President said that a couple of times," White House Deputy Press Secretary Eric Schultz said.
"We are not going to be in a position to defend or criticise the FBI Director. That is our view. But what is also true, and what Josh said on Monday and what the President reiterated yesterday, is that we do take seriously these longstanding norms and customs that historically limit the sort of public speculation and public discussion of facts and materials that are collected in the context of a law enforcement investigation," Schultz told reporters.
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