Trump made a pledge during the campaign to "drain the swamp" of lobbyists and has been dogged by questions about Flynn and both his lobbying work and ties to Russia.
"Just so we're clear, is that a personal lawyer of General Flynn's contacted a transition lawyer and asked for guidance on what he should or should not do," Spicer said today. "The lawyer was instructed that at -- that that wasn't the role of the transition and that it was up to the personal lawyer to work with the appropriate authorities or subject matter experts to determine what was appropriate and what was not appropriate in terms of filing. This was a personal matter. It's a business matter."
But Vice President Mike Pence -- the chairman of the transition team -- said that the first time he heard of the lobbying ties was this week and not during the transition.
Two senior administration officials tell ABC News that the Turkey issue was not one of the aforementioned "series of questionable instances" Spicer said last month led Trump to ask for his resignation.
A source familiar with the situation tells ABC News Flynn informed the White House counsel team both during the transition and after the inauguration that he would have to file as a foreign agent because of the work he did on behalf of the Turkish government.
This source could not say if Flynn first made the team aware of his situation before or after President-Elect Trump announced that he be appointing the former general to be his NSA on Nov. 18th.
In a letter, dated March 7, a lawyer for the Flynn Intel Group told the Foreign Agents Registration Act (FARA) division of the DOJ that the company had done work on behalf of a Dutch client, Inovo BV.
The work was disclosed in September 2016, and Flynn's group terminated its contract and ceased operations after his appointment, the letter says. A public disclosure was filed on Dec. 1, 2016, according to the letter.
The group had planned to file under the Lobbying Disclosure Act, but decided it was not appropriate.
"Nevertheless, because of the subject matter of Flynn Intel Group's work for Inovo BV, which focused on Mr. Fethullah Gulen, whose extradition is sought by the Government of Turkey, the engagement could be construed to have principally benefitted the Republic of Turkey," the letter said. "To eliminate any potential doubt, the Flynn Intel Group therefore is electing to file a registration under FARA, in lieu of its prior LDA registration."
Gulen is a Turkish cleric who lives in the United States. He was blamed by the Turkish government for a failed military coup there last July.
Trump asked for Flynn's resignation in February after the former general misled Pence and other administration officials about his conversations with the Russian ambassador, which included sanctions being placed on that country. After the resignation, Trump blasted the media for treating Flynn "very, very unfairly" and called him a "wonderful man."
Spicer said today that the president was not informed of "this arrangement" or his need to register as a foreign agent.
It was not clear if "this arrangement" referred to Flynn's lobbying in general or the specifics of the arrangement.
Spicer also said there should be no concerns that others in the administration have similarly lobbied on behalf of foreign governments, suggesting that Trump "made the right call" regarding Flynn back when he asked for his resignation over misleading the vice president.
ABC's Jonathan Karl and Justin Fishel contributed reporting to this story.