Beyond the issue of refugees, some observers worry that the US migrant deal with Uganda could create additional challenges for the country as it approaches next year's presidential election.

"The agreement between the US and Uganda may shield the Ugandan government from critical scrutiny regarding its authoritarian practices, particularly as the country approaches a general election," Nicodemus Minde, a researcher at the Institute for Security Studies think tank, told CNN.

Since returning to the White House, Trump has accelerated deportations of undocumented migrants to third countries. In July, five men were sent to Eswatini and eight to South Sudan, while hundreds of alleged Venezuelan gang members were transferred to El Salvador before being returned home. Rights groups warn these actions may breach international law.