She also had an additional phone call with the White House.
Yates said she expected the White House to act on the information she conveyed.
She was sacked four days later by the Trump administration.
"Not in the course of the preparation of the intelligence communities assessment", said Mr Clapper, who served under former President Barack Obama. He retired when Trump took office.
Yates told a Senate Judiciary subcommittee on Monday that she warned the White House about Flynn's conversations with Kislyak so that the Trump administration "could take action" amid concerns Flynn could have been subject to blackmail. Apparently Trump believed that Obama commented about it "in jest".
Flynn's conversations with Russian Ambassador Sergey Kislyak caught the attention of Trump's own transition team.
On Tuesday, Press Secretary Sean Spicer was required to answer multiple questions about ousted National Security Advisor Michael Flynn and the nature of his hiring by Donald Trump's administration. Why?
Obama pushed Flynn out in 2014 from his job as director of the military's Defense Intelligence Agency, or DIA.
Monday, CBS News also confirmed former President Obama counseled then-President-elect Trump to pick another national security adviser immediately after the election. Spicer later denied that Yates showed serious worry about Flynn's call, and said she simply gave "a heads up" about it.
She said Monday she did not - and that she had revealed no classified information herself.
Trump repeatedly has said he has no ties to Russia and isn't aware of any involvement by his aides in any Russian interference in the election.
The subpoenas represent the first sign of a significant escalation of activity in the FBI's broader investigation begun last July into possible ties between Trump campaign associates and Russian Federation. And in almost every single one, the top Democrat on the committee spends time outlining the Trump administration's connections to Russian Federation, as Sen.
Then in late December or early January, someone working under Obama's own national security adviser, Susan Rice, unmasked routine NSA intercepts of the Russian ambassador.
The warning was "based on Flynn's role as head of DIA", a former administration official told the AFP.
INSKEEP: So what did Sally Yates fully put on the record here about Michael Flynn?
Trump has repeatedly branded the issue of Russian interference "fake news" despite leaders of the United States intelligence community concluding that President Vladimir Putin himself was behind the meddling.
Yates herself, a longtime federal prosecutor, was sacked by Trump on January 30 after refusing to defend his travel ban.