In an interview with Fox News' Eric Shawn, Bolton questioned why FBI Director James Comey said during the investigation of Hillary Clinton's private server, there was no direct evidence found of foreign intelligence service penetration, but cyber fingerprints were found in regards to the presidential election.
Shawn then asked Bolton — who has been mentioned as a possible Trump appointment — if he was accusing someone in "the administration or in the intelligence community of" the alleged false flag.
"We just don't know," Bolton said. "But I believe that the intelligence community has been politicized in the Obama administration to a very significant degree."
A "false flag" is a term for a cover-up or distraction orchestrated by the government or other powerful figures.
Shawn continued to push Bolton, asking why intelligence officials would politicize the hack and would "go so far to something that could damage the very issue of our Republic and what we for 200-plus years have stood for."
"The whole thing has been called into question, which is why the notion of some kind of independent investigation becomes extremely important," Bolton said. "I do think it's critical to answer the question that I posed: If you think the Russians did this, then why did they leave fingerprints?"
Last week, the Washington Post published a report saying the intelligence community believes that Russia was favoring Trump to get elected.
President Barack Obama has requested a review of the situation. A bipartisan group of senators (John McCain, Lindsey Graham, Chuck Schumer, and Jack Reed) has also called on an independent investigation of Russian meddling in the U.S. election.
During the interview, Bolton said he had concerns about Obama trying to get the review wrapped up by Jan. 20. He said he thinks the burden of the review will fall on Mike Pompeo, Trump's nominee for director of the CIA.
"He doesn't bring any baggage to this, I would look to him to head up an investigation across the entire intelligence community," Bolton said.
The former United States ambassador said that if the claims about Russia were true, the U.S. "should retaliate."
"It is unacceptable for the American Constitution to be assaulted by foreigners in that way. So it is absolutely critical as well that we get the facts right on this, and I don't think we have anywhere enough in the public domain to know what the facts are," he said.
When asked by Shawn about those who could be bothered by the false flag claim, Bolton said there needs to be more information as to how the intelligence community came to the conclusion.
"We would want to know who else might want to influence the election and why they would leave fingerprints that point to the Russians," Bolton said. "That's why I say until we know more about how the intelligence community came to this conclusion, we don't whether it's Russian inspired or a false flag."