She said that Flynn had a conversation with Vice President Mike Pence but that the information he gave at that time "turned out to not be true."
"I'm not here to say who knew what when," Conway said, after being repeatedly pressed on what Trump and Pence knew regarding Flynn's call to the Russian ambassador before the inauguration. "I don't know all the details."
The president "is a very loyal person," Conway said.
Retired Army Lt. Gen. Keith Kellogg was named acting national security adviser to replace Flynn, who admitted in his resignation letter that he "inadvertently" gave "incomplete information" about multiple calls with the ambassador.
Flynn previously denied that he spoke with the ambassador in December about sanctions the United States imposed on Russia for its suspected interference in the 2016 presidential election — a discussion that may have violated federal law.
Pence repeated the denial when asked about the situation in January, but administration officials noted that he was relying on information provided to him by Flynn.
Sources in the administration confirmed that the Justice Department, under the direction of then-acting Attorney General Sally Yates, informed the White House in January that Flynn may have misled Pence and other senior officials about his communications with the ambassador.
Conway praised Flynn's resume and said he had an "honorable career in the military" that lasted over 30 years.
ABC News' Adam Kelsey contributed to this report.