Noem, who is overseeing President Donald Trump's immigration crackdown, was pressed about her statements by Democrats and some Republicans during a Senate Judiciary Committee hearing on Tuesday.
Shortly after Renee Good and Alex Pretti were slain in separate incidents in January, Noem said they had appeared to have been involved in acts of domestic terrorism before a full investigation into the events that led to their deaths.
Video evidence subsequently undercut her assertions, and her remarks were criticised by lawmakers from both parties.
Senator Dick Durbin, the top Democrat on the committee, repeatedly asked Noem if she would retract her statements concerning Good and Pretti, as well as her similar remarks about another US citizen who survived after being shot five times in a confrontation with federal agents in Chicago.
"I was getting reports from the ground, from agents at the scene," Noem testified, calling the situations chaotic but declining to retract or apologise for her statements.
"I absolutely strive to provide factual information."
Noem, appointed by Trump last year, faced tough questions from senators about Trump's aggressive immigration enforcement tactics during the hearing, her first congressional appearance since Good and Pretti were killed.
The outrage caused by their deaths prompted the Trump administration to shift its strategy, moving away from large-scale, city-focused surges and toward a more targeted approach.
Under Noem, thousands of masked federal agents have been deployed to US cities, where they have swept through neighbourhoods in search of possible immigration offenders and clashed with residents and protesters.
Congressional Democrats have refused to agree to new funding for her department without changes to immigration enforcement practices.
Funding for the 260,000-employee department lapsed last month, but most of its immigration enforcement and national security operations are deemed essential and continue.
Noem said on Tuesday 650 federal agents remain in Minnesota, down from about 3000 in January.
Senator Chuck Grassley, the committee's Republican chairman, acknowledged in opening remarks that "mistakes have been made" by the administration but defended immigration officers, saying they "should never be threatened or harmed while enforcing our laws."
House Democrats launched an effort in January to impeach Noem, saying immigration agents under her leadership have violated the civil rights of US citizens, that she had blocked congressional oversight of detention centres for migrants, and she gave government contracts to Republican-affiliated firms and people connected to close associates of hers.
