While the senator did not hear the gunshots outside, two of his colleagues were outside and described to him how they were told to "hit the dirt."
Senators Sherrod Brown, and Bob Casey were also outside the building when police rushed them back inside for safety.
"We thought we heard shots, saw a lot of police cars," explained Ohio Sen. Sherrod Brown.
"We heard pops that sounded like shots," said Sen. Bob Casey of Pennsylvania.
"We heard pops -- 3,4,5 -- I don't know if they were shots or not," Brown said.
Capitol police confirmed Thursday afternoon shots were fired in two locations as officers tried to stop a speeding Infiniti racing toward Capitol Hill.
Just before the chase, the driver had tried to ram through the security barricade at the White House.
It's not something you see every day. You see a lot of officers around, you see them with guns but not ready to fire," Flake said.
While detectives search for answers, police do believe this was an isolated event.
But retaliation for a government shutdown crossed some minds.
"I think that went through everyone's mind, whether they admit it or not. You think that somebody disgruntled about that... or the Navy Yard shooting that happened just a couple of weeks ago," Flake said.