Flynn's consulting company, Flynn Intel Group Inc., received $530,000 from a Turkish company for work that "could be construed to have principally benefited the Republic of Turkey" according to the Department of Justice's Foreign Agents Registration Act (FARA) filings.
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.
Flynn, who resigned from his job for misleading Vice President Mike Pence about phone conversations he has with Russia's ambassador to the USA, has since been found to have been paid around $530,000 (£435,000) lobbying for a company owned by a Turkish businessman that could have aided Turkey's government.
Flynn, a retired U.S. Army lieutenant general and former director of the Defense Intelligence Agency, served as national security adviser for 24 days before resigning on February 13 after it was revealed that he misled White House officials regarding conversations he'd with Russian ambassador to the U.S. Sergey I. Kislyak.
The new details follow remarks Thursday by Vice President Mike Pence, who said he was unaware of Flynn's foreign agent work until this week.
And Mr Pence seemed less forgiving than Mr Spicer. Alptekin acknowledged he helped arrange a meeting between Flynn and Turkish officials, including two cabinet ministers. Flynn shut his firm down in November.
In the opinion piece, Flynn paints Fethullah Gulen, the USA based cleric whom Erdogan blames for the coup attempt, as a "radical Islamist".
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After his firm's work was done, Flynn agreed to not lobby for five years after leaving government service, and never to work on behalf of foreign governments again.
Finally registering the work in March, Flynn Intel Group stated that Inovo previous year had represented a private company in Israel that sought to export natural gas to Turkey.
But documents filed this week by Flynn with the Department of Justice paint a different picture.
The White House had been unclear about when it was told of Flynn's lobbying that may have aided the Turkish government. "What does this say about the transition team's judgment about still appointing him as national security adviser when you had knowledge of this information?"
HR McMaster was appointed as Flynn's replacement as national security adviser last month.
According to an editor's note added to the post on Thursday, the Turkish firm paying Flynn reviewed his essay before it was submitted.
Spicer argued it's "not a question of raising a red flag", insisting it's not legal or appropriate for the government to "start going into private citizens seeking advice and telling them what they have to register or not".