White House press secretary Sean Spicer said Friday that Flynn's attorney contacted a Trump transition attorney to notify the transition of the potential filing, but said Trump was not made aware. Separately, Vice President Mike Pence, who headed up the transition, was notified in a November letter from the top Democrat on the House oversight committee that Flynn's firm had lobbied on behalf of a foreign power.
Spicer rejected questions about whether the disclosures should have raised red flags about Flynn, saying "it's not a question of raising a red flag."
But Flynn's Justice Department filing, which revealed that Flynn's firm worked on behalf of a Turkish-owned company to improve US confidence in Turkey's business climate, raised further questions about Flynn, who was forced to resign from his role as national security adviser last month.
Flynn's resignation came after a report alleged that he had discussed US-imposed sanctions against Russia with the Russian ambassador to the US
during the transition and failed to disclose that part of his conversation to Pence. Flynn maintains he doesn't remember discussing the sanctions and Russian officials deny that the topic came up.
Flynn's consulting firm, FlynnIntel Group, received $530,000 in payments from a Turkish-owned company based in the Netherlands and this week registered as a foreign agent with the Justice Department, acknowledging that the work may have benefited the Turkish government, according to foreign agent registration paperwork filed with the Justice Department.
The work came at the height of the US presidential campaign and while Flynn served as Trump's top foreign policy adviser on the campaign. The contract did not end until November 15 , a week after Trump was elected president.
Pence on Thursday called the news of Flynn's foreign agent filing "an affirmation of the President's decision to ask General Flynn to resign" in an interview with Fox News.
A source familiar with the filing told CNN earlier Friday that the Trump transition was notified Flynn would likely file the foreign agent paperwork and that the White House Counsel's Office was later notified after the inauguration.
Flynn's firm was not compensated by the Turkish government, but by Inovo BV, a company owned by Turkish businessman Ekim Alptekin, according to the Justice Department filing. Alptekin is also the chairman of a US-Turkish business council.
However, as part of the project, Flynn met with a group of Turkish government officials in September 2016, including Turkey's ministers of foreign affairs and energy, the firm disclosed in the filing. The meetings came around the time when Flynn traveled regularly with Trump on his private plane and frequently introduced him at campaign rallies.
Flynn also wrote an editorial that was published in "The Hill" newspaper
on Election Day that called on the US to oust an anti-Turkish government cleric living in exile in the US. Flynn's firm acknowledged in the Justice Department filing that the op-ed was compiled using research paid for as part of the Turkish project, which Flynn did not disclose at the time of the op-ed's publication.
Alptekin told CNN on Friday that his firm is in no way funded by the Turkish government and said he contracted Flynn's firm because "my company has clients that are best served when Turkish-American relations enjoy continuity."
Alptekin said Flynn "made no representation about what he would do for Turkey" in a potential US admininstration and said he "did not say a single word about any position that he would occupy." Still, Alptekin said he made clear how he felt the US-Turkey relationship should be managed, including under a Trump presidency.
Alptekin said he has not talked to Flynn or his lawyers about the foreign agent filing, but said he consulted with a lawyer about the matter who did not believe it was necessary to file the registration.
"I think it was an abundance of caution to do that," he said. "I really have difficulty understanding the turmoil."