Robert Kelley, a former chief counsel to the House National Security Subcommittee and current general counsel and principal at the Flynn Intel Group, filed a lobbying disclosure report with Congress on September 15.
According to the official document, Kelley was working on behalf of Inovo BV, a Dutch firm owned by Turkish businessman, Kamil Ekim Alptekin.
Alptekin told CNN in an email that the firm works to strengthen "the transatlantic relationship and Turkey's future in that alliance."
Kelley's connection to the Flynn Intel Group and Alptekin were first reported in the Daily Caller.
Ranking Member of the House Committee on Oversight and Government Reform Elijah Cummings sent a letter to Trump transition chair Mike Pence expressing concerns over Flynn's "apparent conflict of interest."
"President-elect Trump promised during his campaign that he would 'drain the swamp,' but his top national security advisor is Lt. Gen. Michael Flynn, whose firm is reportedly being paid to lobby the U.S. Government by a close ally of Turkey's president," the Maryland Democrat wrote. "It is unclear how Lt. Gen. Flynn was reportedly allowed into intelligence briefings during the campaign despite these apparent conflicts of interest."
Trump's transition responded to questions about the lobbying effort with a statement Friday, saying that Flynn's career was within his right as a "private citizen."
"After devoting his life to serving his country, Lt. Gen. Michael Flynn became a private citizen and opened a private consulting business to advise companies on various issues. Gen. Flynn has said that he will sever ties to his consulting firm if he ever returned to government service and that is what he will do in the Trump Administration."
Alptekin is the chair of the Turkish-American Business Council and helped organize Turkish President Recep Erdogan's 2015 visit to Washington.
But while Alptekin acknowledged having a commercial relationship with the Flynn Intel Group, he told CNN that Flynn himself "does not work on my contract."
He also adamantly denied any connection to the Turkish government.
"Neither Inovo, any of my other companies or my person are affiliated to the Turkish government in any form whatsoever," he said.
He added that his company's contract with Flynn's company "is not about representing the position of the Government of Turkey"
However, the fact that Flynn was overseeing a company that was lobbying on behalf of foreign clients at the same time he was attending classified briefings alongside Trump seems to complicate the transition, especially given Trump's stated goal of "draining the swamp" in Washington.
Flynn, who as America's top military intelligence officer was already privy to volumes of classified material, is obligated to not share that information with any outside entity.
While Flynn had the highest level of clearance while serving as the director of the Defense Intelligence Agency, experts on security clearances told CNN that his firm's business arrangements with foreign companies would be closely looked at by background investigators before Flynn could receive additional intelligence briefings in his new role.
"They would certainly look at it carefully," Sean Bigley, a security clearance lawyer and former government background investigator told CNN.
Although Bigley said there was no restriction on someone like Flynn working for foreign companies upon leaving office he said Flynn would have to inform background investigators of these business relationships in order to be able to continue to receive classified briefings.
But other lawyers specializing in security clearance issues said Flynn simply informing investigators of his company's ties to Inovo might not protect him from having his security clearance revoked.
Bradley Moss, an attorney who routinely represents defense contractors in security clearance disputes, said Flynn's actions would likely raise a red flag.
Flynn's lobbying work, according to Moss, could potentially jeopardize his ability to get cleared as national security advisor.
"Security adjudicators would have concerns that someone with Flynn's level of experience wouldn't think twice about sitting in on a classified briefing while working for foreign clients," Moss said. "The moment he sat in on classified briefings, his association with his own company had to be severed."
"By not doing that he exposed himself unnecessarily to foreign influence and raised questions about his good judgment," Moss added.
Asked about Flynn's business dealings, CNN counterterrorism analyst Phil Mudd told CNN's Wolf Blitzer Friday that that type of work was not unusual and that his activities should not prevent him from taking on the role of national security advisor.
"I don't think those should be a bar to duty," he said.
But while he said his business relationships were not disqualifying, Mudd, a former CIA analyst, said Flynn's temperament would not serve him well in the role.
The intelligence briefs containing some classified were first given to both candidates in August and Flynn accompanied Trump during at least one brief. It is unclear if Flynn informed investigators of his company's ties to Inovo. His representatives did not reply to a request for comment.
Flynn told the Wall Street Journal that if he were to officially join the Trump administration he would sever ties with his company, which is described as providing "all source intelligence support to global challenges."
"If I return to government service, my relationship with my company will be severed in accordance with the policy announced by President-elect Trump," he said.
Flynn's connection to Turkey drew scrutiny after he penned an Election Day op-ed in The Hill newspaper, which said the US should extradite the exiled cleric Fetullah Gulen to Turkey.
The Turkish government has accused Gulen of being behind the July coup and has demanded the US hand him over. The Justice Department is currently reviewing the case for extradition.
But Alptekin said he and his company had nothing to do with Flynn's op-ed.
"If he had asked me whether to publish it, I would have advised against it for a variety of reasons," he said.