Obama's remarks in an interview with website NowThisNews were his first public comments since Comey's announcement Friday that the FBI had discovered a new trove of emails that might or might not be pertinent to an earlier probe of Democratic candidate Hillary Clinton's handling of classified information.
"I've made a very deliberate effort to make sure that I don't look like I'm meddling," Obama said, before making his veiled criticism of Comey's handling of the affair without mentioning him by name.
"I do think that there is a norm that when there are investigations we don't operate on innuendo, we don't operate on incomplete information, we don't operate on leaks," he said.
Comey has come under fierce criticism from Democrats for effectively reopening the Clinton probe so close to the November 8 elections, without knowing whether the new email were relevant.
Comey's announcement was a departure from Justice Department policy not to comment on ongoing investigations or to take actions close to elections that could influence the outcome.
In July, Comey had recommended against bringing charges against Clinton after a long investigation into her use of a private server to send email while secretary of state.
Republicans were outraged at the FBI director's stance at the time, but Republican nominee Donald Trump has hailed Comey this time for reporting the email find to members of Congress.
"We operate based on concrete decisions that are made," Obama said.
"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.
Comey has provided no timetable for concluding the review of the latest emails.
FBI agents are sifting through hundreds of thousands of emails found on a laptop taken in a separate investigation from Anthony Weiner, the estranged husband of close Clinton aide Huma Abedin.
RELATED READING
Hawkins responds to Trump video with defence of billionaire
