"Why don't you have solutions?" "We need to shut it down", he demanded.
Administration officials spoke on the condition of anonymity to provide a candid account of the private meeting.
During his 2016 presidential campaign, Trump fervently pushed for immigration reform by outlining bold plans, including the construction of a massive wall stretching across the US-Mexico border. Eventually, the topic moved on to health care, bringing relief to many in the room.
According to The New York Times, the president complained his administration has to do more on border security.
White House press secretary Sarah Sanders was asked about the incident in Thursday's press briefing.
Nielsen battled back, one person said, telling Trump that laws limit some of what she could do to block the flow of undocumented immigrants.
A senior administration official confirmed the incident to Reuters, saying: "He lit into her". The president urged Nielsen to be more aggressive, the official said.
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But they have not won a game for nearly two months. "They were emotion as a outcome of winning this key game". The victory was sufficient for his side to avoid being relegated to the Championship.
The exchange was so hostile, according to The New York Times, that Nielsen later informed colleagues that she planned to leave the administration and drafted a resignation letter, though she did not submit it. In a statement Thursday, a spokesman for the agency said that was false.
Another key player in the Trump administation may have come close to resigning her post this week, after the president lashed out at her in a Wednesday meeting.
Trump has growing increasingly angry about his inability to secure the border and has repeatedly called on Congress to pass new legislation to strengthen what he calls the nation's "horrible" immigration laws.
Homeland Security's deputy secretary position is vacant, so there would be no immediate replacement if Nielsen were to step down.
A Homeland Security spokesperson denied the claims that Nielsen had drafted a resignation letter and was close to resigning. He reminds staff that she was a "George W. Bush person" because of her previous tenure as a White House Homeland Security adviser.
Along with the some 700,000 Dreamers brought to the USA illegally as children, who Trump stripped of protection in September, about one million people who were once legal residents in the country face potential deportation. Families are typically broken up in those circumstances, as federal immigration agents send children to government shelters while their mothers and fathers remain in custody awaiting court dates.
Trump has also been frustrated with Nielsen, according to people familiar with the dynamic.
"We should fold all of the TPS people that have been here for a considerable period of time and find a way for them to be on a path to citizenship", Kelly, one of President Donald Trump's top aides, said in an interview.