The move alarmed Democrats after they had raised concerns that White House involvement could further politicize what is supposed to be an independent probe.
Responding to questions about why Flood and Kelly were there, White House press secretary Sarah Sanders issued a statement saying "Neither Chief Kelly nor Mr. Flood actually attended the meetings but did make brief remarks before the meetings started to relay the President’s desire for as much openness as possible under the law."
"They also conveyed the President’s understanding of the need to protect human intelligence services and the importance of communication between the branches of government. After making their brief comments they departed before the meetings officially started," her statement continued.
"The President personally wanted Emmet there today," Giuliani told ABC News.
Giuliani says he and the full Trump legal team have not yet had a readout of what information was learned but they look forward to a briefing. shortly.
A congressional source said after Flood and Kelly delivered remarks at the top of the meeting, "it was expressed to them how inappropriate their presence was."
Rep. Adam Schiff, D-Calif., the top Democrat on the House Intelligence Committee, acknowledged that Flood didn't take part in the briefings, but said his presence was "completely inappropriate," and that he "made this clear" to Flood.
Nunes and Gowdy left about an hour later without speaking to reporters.
Ryan later put out a statement referring to the House Intelligence Committee Nunes chairs, saying "Inherent in the committee’s work is the responsibility to ask tough questions of the executive branch. That is why we have insisted and will continue to insist on Congress’s constitutional right to information necessary for the conduct of oversight."
Kelly had helped arrange what was originally planned as just a DOJ briefing for Nunes and Godwy as Republicans continue to spar with the Justice Department on requests for documents and information related to a myriad of GOP investigations into the department.
The meeting comes as President Trump continues to stoke unsubstantiated claims that the FBI planted a spy inside his presidential campaign. He has said the briefings could provide proof of his unsubstantiated claim the FBI was likely spying on his campaign.
“A lot of bad things have happened. We now call it ‘Spygate,’” Trump said as he departed the White House Wednesday. Countering Trump, Schiff has said the controversy should be called "Lie-gate."
"Nothing we heard today has changed our view that there is no evidence to support any allegation that the FBI or any intelligence agency placed a spy in the Trump campaign, or otherwise failed to follow appropriate procedures and protocols,” Schiff said.
Later, Senate Majority Leader Mitch McConnell told Fox News that there was "nothing really surprising" in the classified briefing.
Following protests from top Democrats and Republicans, the White House arranged the second briefing.
The meetings are the result of a subpoena Nunes issued earlier this month demanding classified documents related to the source, a request the Justice Department denied over national security concerns.
After Nunes threatened to move to hold Attorney General Jeff Sessions in contempt of Congress over the refusal, the Justice Department invited Nunes and House Oversight Committee Chairman Trey Gowdy to DOJ for a briefing on the documents.
On Sunday, Trump entered the fray, calling for the DOJ to investigate whether the FBI “infiltrated or surveilled” his presidential campaign and whether it was ordered by Obama administration officials – allegations he has not backed up with evidence.
The Justice Department subsequently directed the DOJ inspector general, the agency's watchdog, to expand its ongoing investigation of surveillance of Trump campaign adviser Carter Page during the presidential election to include the president's concerns.
Nunes has said the request relates to classified information relevant to his ongoing investigation into allegations of political bias at the Justice Department related to the Russia investigation. It remained unclear Thursday if Nunes received the information he sought. He declined to comment Thursday following his first briefing.
Some Republicans have suggested moving forward with a proposal to hold Rosenstein in contempt of Congress if DOJ did not provide the information Nunes and Gowdy were seeking.
Democrats continue to express concern about the initial disclosure of the reported informant. Rep. Jerry Nadler, D-N.Y., the top Democrat on the House Judiciary Committee, has asked the Justice Department and FBI to investigate the source of the disclosure that first appeared in media reports.
"Somebody has outed an intelligence asset for what seem to be purely political purposes," he wrote, after raising "concerns" earlier in the day that it was a member of Congress who leaked information about the informant to the media.
ABC News' Cecelia Vega, Trish Turner, Devin Dwyer, John Santucci and Mariam Khan contributed to this report.