Lake told host Mark Levin that the relationship between Flynn and former President Barack Obama was "very strained because Michael Flynn, when he was ... the director of the Defense Intelligence Agency [DIA], beginning in Obama's first term, he began pushing back against Obama's negotiations on the Iran nuclear deal."
Flynn spent two years as director of the DIA, leaving that position in August 2014.
Lake added that Flynn "was very skeptical of intelligence programs [aimed] to find what are known as moderate rebels in Syria to fight against the regime of Bashar al-Assad.
"He believed those so-called moderate rebels were really either going to collaborate or had collaborated with Al Qaeda, and in some cases, ISIS," Lake said. "And he became very skeptical of that."
After Flynn left the DIA, Lake said the now-retired Army lieutenant general may have ruffled feathers in Washington with a pair of interviews in which he expressed concerns about the Obama administration's Syria policy.
"This, I think, infuriated the intelligence community," he said. "The CIA had a program and the Pentagon had a program in this regard, and that was also part of it."
Lake went on to say that another point of contention between Obama and Flynn developed in the aftermath of the 2011 raid that killed Usama bin Laden. The columnist said Flynn was strongly concerned that Obama saw bin Laden's death as a good point to wind down the War on Terror.
"In that crucial period, if you remember back in 2013 and 2014, that really seemed to be the Obama administration's approach. And I think that Flynn thought that was a huge mistake," he said.
"So, all of these internal disagreements, I think, led to his premature ouster as the director of the Defense Intelligence Agency. And also meant that some of the traditional benefits for people who retire from the national security state at the level that Mike Flynn was, were not on offer for him," Lake further claimed.
According to Lake, Flynn was not given opportunities handed to other decorated retired generals, such as the chance to serve on corporate boards.
"In my view, that's not an excuse necessarily for some of the decisions he made with his own consulting group," he said. "But it's part of the way to explain some of that and what happened in this period before 2016."