Ms Omar responded on Twitter, telling Mr Trump: “You are stoking white nationalism (because) you are angry that people like us are serving in Congress and fighting against your hate-filled agenda.”
The president's comments were condemned almost unanimously by Democrats as well as by several members of his own party.
Mitt Romney, a Republican senator in Utah who was the party's presidential nominee in 2012, said Mr Trump's language was “destructive, demeaning, and disunifying.”
Jewish groups also criticised the tone of the president's remarks.
“As Jews, we are all too familiar with this kind of divisive prejudice,” said Jonathan Greenblatt, chief executive of the Anti-Defamation League.
“While ADL has publicly disagreed with these congresswomen on some issues, the president is echoing the racist talking points of white nationalists and cynically using the Jewish people and the state of Israel as a shield to double down on his remarks.”
He added: “Politicising the widespread, bipartisan support for Israel and throwing around accusations of antisemitism is damaging to the security of Israel and the Jewish community. He should lead by example, stop politicising these issues and stop smearing members of Congress.”
The liberal Jewish group J Street said it was "appalled by the ongoing torrent of racist incitement that President Trump continues to direct against progressive women of colour in Congress."
A statement released by the group continued: “We refuse to allow the real threat of antisemitism to be weaponised and exploited by those who themselves share a large part of the responsibility for the rise of white nationalist and antisemitic violence in this country.”
In Britain, the Board of Deputies president Marie van der Zyl said Mr Trump's remarks were “appalling and unjustifiable”.
She said: “Whatever one’s political disagreements, telling people to ‘go back home to where they came from’ can never be the right response. It is also wrong to drag Israel in to these undignified tirades.”
