Last month, Trump said he planned to end the Temporary Protected Status (TPS) - a programme for immigrants from countries in crisis - for Somali residents living in Minnesota. A few hundred immigrants would be affected by that order.
TPS for Somalis has existed since 1991, resulting from conflict in the nation.
Earlier this week, Trump's Homeland Security Secretary Kristi Noem suggested her agency would target visa fraud in Minnesota.
And his US Treasury Secretary Scott Bessent also announced an investigation into allegations that tax dollars from the state may have been diverted to the al-Shabab Islamist militant group in Somalia, which is part of al-Qaeda. The probe follows unverified media reports in the US, which have been denied by the militants.
Somalia is one of the poorest nations in the world, and many of the migrants who moved to the US left in the 1990s during the country's decades-long civil war.
Asked by a reporter about Trump's comments, Somali Prime Minister Hamza Abdi Barre said he not personally heard them but had been briefed about them. He pointed out that Trump had not only spoken about Somalia, but had made similar remarks about other African countries, notably Nigeria and South Africa.
The prime minister said his government preferred not to elevate the issue.
"There are things you pass with 'Salaaman'," he added, using a Qur'anic expression meaning responding to offence with peace rather than confrontation.
"Making an issue out of it and giving it importance is more harmful than simply moving on," he said.
Meanwhile, local leaders in Minnesota have directly condemned the Trump administration's reported plan for an ICE operation.
Minnesota state Senator Zaynab Mohamed said on X that "when ICE agents interact with Somalis here, they will find what we've been saying for years: Almost all of us are US citizens".
Democratic Minnesota Governor Tim Walz, who was Kamala Harris's running mate in the 2024 presidential election and who has been sparring with the president in recent days, said: "We welcome support in investigating and prosecuting crime. But pulling a PR stunt and indiscriminately targeting immigrants is not a real solution to a problem."