Flynn acted as a foreign agent representing the interests of Turkey’s government in exchange for more than $500,000 during last year’s presidential campaign even as he was advising Trump, the New York Times said on Friday.
White House spokesman Sean Spicer told reporters Flynn's lobbying was a personal and business matter, and it was up to him to decide when to register.
Asked if Trump had not been aware that former general Flynn was working as a foreign agent, Spicer said: "Correct... You wouldn't know that until he filed. He didn't file until two days ago."
Some U.S. lawmakers have questioned Flynn's relationship with the government of Turkish President Recep Tayyip Erdogan. Before Trump's inauguration, Flynn's ties to Turkey were widely reported and he wrote an article urging the United States to cultivate better relations with Erdogan.
Trump fired Flynn last month for discussing U.S. sanctions on Russia with the Russian ambassador to the United States before Trump took office on Jan. 20 and misleading Vice President Mike Pence about the conversations.
Before Trump took office, Flynn's lawyer contacted the presidential transition team about his work for Turkey to ask what he should do, Spicer said. The lawyer was told "it was up to the personal lawyer to work with the appropriate authorities ... to determine what was appropriate and what was not appropriate in terms of filing," Spicer said.
"We trust people to fill out the forms that they are required to do so in an honest and legal manner, and in this case he retroactively filed the forms he was supposed to do," he said.
"We did the right thing then, and we expect every employee to follow the law."
Spicer said he did not know whether Flynn had disclosed his lobbying work in the security clearance review before he became national security adviser.
(Reporting by Washington Newsroom; Editing by Alistair Bell)