In recent days, the New York Times and the Associated Press clarified that three major U.S. intelligence agencies – and not 17, as the news agencies repeatedly reported – assessed that Russia attempted to interfere in the 2016 presidential election.

While the U.S. Intelligence Community is indeed made up of 17 agencies, the actual January 6, 2017 U.S. Intelligence Community report alleging Russia interference was the product of only three – the FBI, CIA and National Security Agency.

In its clarification, the Times wrote that the Russia interference conclusion was drawn by “four intelligence agencies” – including James Clapper’s Office of the Director of National Intelligence, which issued the January 6 report although its conclusions were not included in the report itself.

At the time of the assessment, the FBI was led by James Comey, who was fired following controversy over his handling of Hillary Clinton’s email probe, and the CIA was headed by Barack Obama appointee John Brennan.

Below are five significant issues with the official assessment as compiled by the CIA, FBI and NSA (and not 17 agencies) regarding alleged Russia interference.

1 – The NSA did not share the “high confidence” of the CIA and FBI.

The NSA did not share the “high confidence” of the CIA and FBI in the conclusion of the January 6 U.S. Intelligence Community report alleging the Russian government sought to aid Donald Trump’s “election chances when possible by discrediting Secretary Clinton and publicly contrasting her unfavorably to him.”

The NSA endorsed that conclusion with “moderate confidence.”

In testimony in March, former NSA Director Mike Rogers was asked why his agency only had “moderate” confidence in the judgment. He replied:

I’m not going to get into specifics in an unclassified forum but for me, it boiled down to the level and nature of the sourcing on that one particular judgment was slightly different to me than the others.

Asked by Rep. Mike Conaway (R-TX) during the same March hearing about the FBI’s “high confidence” judgment that Putin favored Trump and was aiming to help him win against Clinton, Comey stated that part of the conclusion came from “logic.”

Here is a transcript of that exchange:

COMEY: I don’t know for sure, but I think that was a fairly easy judgment for the community. He — Putin hated Secretary Clinton so much, that the flipside of that coin was he had a clear preference for the person running against the person he hated so much. CONAWAY: Yeah and that and that my work on Saturday afternoon when the — my wife’s Red Raiders are playing the Texas Longhorns. She really likes the Red Raiders. But all the rest of the time, I mean the logic is that because he really didn’t like president — the Candidate Clinton, that he automatically liked Trump. That assessment’s based on what? COMEY: Well, it’s based on more than that. But part of it is and we’re not getting into the details of it here, but part of it is the logic. Whoever the Red Raiders are playing, you want the Red Raiders to win, by definition, you want their opponent to lose.

Further in the exchange, Comey said the Russians tried to undermine Clinton because the polls showed she was ahead:

CONAWAY: So — and then election then says, the government — the Russian government aspired to help President-elect Trump election chances. So when did they not think she was going to win? COMEY: Well, the assessment of the Intelligence Committee was, as the summer went on and the polls appeared to show that Secretary Clinton was gonna win, the Russians sort of gave up and simply focused on trying to undermine her, it’s your Red Raiders, you know they’re not going to win. So you kind of hope key people on the other team get hurt so they’re not such a tough opponent down the road. And so there was at some point…

In testimony in May, Comey confirmed that the basis for the intelligence community’s assessment that Putin allegedly wanted Trump in office was not because the billionaire was, as Sen. Al Franken (D-MN) claimed during a hearing without citing any evidence, “ensnared in” Russia’s “web of patronage.”

Instead, the FBI chief provided two primary reasons for Russia allegedly favoring Trump over Clinton during the 2016 presidential race.

One reason, according to Comey, was that Putin “hated” Clinton and would have favored any Republican opponent. The second reason, Comey explained, was that Putin made an assessment that it would be easier to make a deal with a businessman than someone from the political class.

Comey’s statements are a far cry from the conspiracies, fueled by the controversial, largely discredited 35-page dossier allegedly paid for by Democrats and anti-Trump Republicans, alleging Putin held blackmail information over the billionaire.

2 – The Obama administration reportedly relied on an outside country for “critical intelligence” claiming Russian interference.

According to the Washington Post, one reasons the NSA’s confidence was lower was because some of the most important technical intelligence used by the Obama administration to allege that Moscow interfered in the 2016 election came from another country.

Those details were buried inside an extensive, 7,700-plus word Washington Post article published two weeks ago entitled, “Obama’s secret struggle to punish Russia for Putin’s election assault.” The piece was based on interviews with over three dozen “current and former U.S. officials in senior positions in government, including at the White House, the State, Defense and Homeland Security departments, and U.S. intelligence services.”

A section inside the article contains this revelation:

Some of the most critical technical intelligence on Russia came from another country, officials said. Because of the source of the material, the NSA was reluctant to view it with high confidence.

3 – A Congressman who reviewed the intelligence disagreed with the CIA’s “high confidence” judgement on Russian interference.

During his questioning of former CIA Director John Brennan at a hearing on May 23, Rep. Christopher Stewart (R-UT) raised a red flag regarding the CIA’s “high confidence” judgement that Moscow sought to aid Trump in the election by attempting to discredit Clinton.

Stewart stated:

And thank you Mr. Director for, again, your many years of service. I’m going to go very quickly because I want to reserve as much time as I can for our task force and the attorneys. I want to go through and make one point; it’s a point worth making. But before I do, I’m just going to add that I’ve reviewed the raw intelligence of the CIA regarding the analysis of whether they preferred Mr. Trump.

I don’t agree with the conclusion, particularly that it’s such a high level of confidence. I just think there should’ve been allowances made for some of the ambiguity in that and especially for those who didn’t also share in the conclusion that it was a high degree of confidence. But having said that, I do think we can agree that Russia wants a weakened U.S. president, would you agree with that?

4 – The Intelligence Community’s report on alleged Russian interference was quickly compiled.

That point was driven home during the following exchange between ex-CIA Director Brennan and Rep. Elise Stefanik (R-NY) during the May testimony:

STEFANIK: Thank you, Mr. Chairman, and thank you, Director Brennan, for your service. My questions will be focused on the process and development of the intelligence community assessment. As you know, the previous administration directed the intelligence community to produce a comprehensive intelligence report assessing Russian activities and intentions on December 9.

The unclassified version of that report incorporated information as of December 29. In your experience as an analyst and as the director, what is the average time that it typically takes to produce an I.C. assessment?

BRENNAN: It can range from days to months to years, in fact, depending on the complexity of the matter, as well as the urgency of getting something out, but it really does vary widely.

STEFANIK: So you noted that the complexity can have an impact on the timeliness to produce a comprehensive report. This report was produced in just 20 days in December. Was there anything about this interagency process that differed the timeline, the approval process, the editing or the staffing?

BRENNAN: I think it followed the general model of how you want to do something like this with some notable exceptions.

It only involved the FBI, NSA and CIA as well as the Office of Director of National Intelligence; it wasn’t a full interagency community assessment that was coordinated among the 17 agencies and for good reason, because of the nature the sensitivity of the information trying to, once again, keep them tightly compartmented.

But in terms of the — the rigor on the — the (inaudible) tradecraft as well as the sourcing and as you think now, in the classified version there, it’s extensively sourced. It tried to adhere to the — the general standards.

Brennan did not further explain his comment that there were some “notable exceptions” to the Intelligence Community’s usual method of compiling such a report.

5 – The intelligence gathering operation, carried out by individuals from within the CIA, NSA and FBI, was said to have been highly compartmentalized and reported in secret to a select grouping of top Obama administration officials. Those officials included Comey and Attorney General Loretta Lynch, two individuals whose actions regarding Clinton’s email probe have been subject to question.

Brennan himself referred (see above testimony) to the “tightly compartmented” operation.

The Washington Post, in its extensive article published two weeks ago (also referenced above), reported on details of the compartmentalized operation that indicates a high degree of secrecy involving top Obama administration officials.

According to the newspaper, in the summer of 2016, then-CIA Director Brennan convened a “secret task force at CIA headquarters composed of several dozen analysts and officers from the CIA, the NSA and the FBI.”

The Post described the unit as so secretive it functioned as a “sealed compartment” hidden even from the rest of the U.S. intelligence community; a unit whose workers were all made to sign additional non-disclosure forms.

The unit reported to top officials, the newspaper documented:

They worked exclusively for two groups of “customers,” officials said. The first was Obama and fewer than 14 senior officials in government. The second was a team of operations specialists at the CIA, NSA and FBI who took direction from the task force on where to aim their subsequent efforts to collect more intelligence on Russia.

The number of Obama administration officials who were allowed access to the Russia intelligence was also highly limited, the Post reported. At first only four senior officials were involved: Brennan, Clapper, Attorney General Loretta Lynch and James Comey. Their aides were all barred from attending the initial meetings, the Post stated.

The newspaper continued :

Gradually, the circle widened to include Vice President Biden and others. Agendas sent to Cabinet secretaries — including John F. Kerry at the State Department and Ashton B. Carter at the Pentagon — arrived in envelopes that subordinates were not supposed to open. Sometimes the agendas were withheld until participants had taken their seats in the Situation Room.

Adding another layer of secrecy, the newspaper reported that when the closed Cabinet sessions on Russia began in the White House Situation Room in August, the video feed from the main room was cut off during the meetings. The feed, which allows only for video and not audio, is usually kept on so that senior aides can see when a meeting takes place.

The paper reported:

The blacked-out screens were seen as an ominous sign among lower-level White House officials who were largely kept in the dark about the Russia deliberations even as they were tasked with generating options for retaliation against Moscow.

Aaron Klein is Breitbart’s Jerusalem bureau chief and senior investigative reporter. He is a New York Times bestselling author and hosts the popular weekend talk radio program, “Aaron Klein Investigative Radio.” Follow him on Twitter @AaronKleinShow. Follow him on Facebook.

With research by Joshua Klein.