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The remark was reportedly in reference to people from Haiti, El Salvador and African countries, the BBC said. Trump told lawmakers the US should instead be taking in migrants from countries like Norway.
In Thursday's meeting, lawmakers were reportedly proposing restoring the Temporary Protected Status (TPS) permits for certain countries, while offering $1.5bn for a wall that Trump wants built on the US border with Mexico.
It continued: "Like other countries that have merit-based immigration, President Trump is fighting for permanent solutions that make our country stronger by welcoming those who can contribute to our society, grow our economy and assimilate into our great nation.
"He will always reject temporary, weak and dangerous stopgap measures that threaten the lives of hardworking Americans, and undercut immigrants who seek a better life in the US through a legal pathway."
Three weeks ago, The New York Times reported that Trump had said Haitians "all have Aids" during a similar June meeting.
Reacting to Trump's remarks on Thursday, Elijah Cummings, a Maryland Democratic lawmaker, tweeted: "I condemn this unforgivable statement and this demeaning of the office of the Presidency."
Mia Love, a Utah Republican and the only Haitian-American in Congress, demanded Trump apologise for the "unkind, divisive, elitist" comments.
The National Association for the Advancement of Colored People (NAACP) accused the president of falling "deeper and deeper into the rabbit hole of racism and xenophobia", the BBC reported.
However, the White House brushed off such criticism.
A Trump official was quoted by CNN as saying: "Though this might enrage Washington, staffers predict the comment will resonate with his base, much like his attacks on NFL players who kneel during the National Anthem did not alienate it."
This week the Trump administration announced it was withdrawing TPS for more than 200,000 people from El Salvador. It means Salvadoreans living in the US for last three decades have until next year to leave, seek lawful residency or face possible deportation.
They were granted provisional US residency after an earthquake devastated the Central American nation in 1991. The State Department said on Monday that much of it has since been repaired.
TPS permits have already been withdrawn from Haitians and Nicaraguans.
With this, hundreds of thousands of migrants face possible deportation from the US, the BBC said.