The US Department of Homeland Security reported that there were already 64 people who took a government-funded flight to their home countries as part of a new programme encouraging undocumented immigrants to "self-deport."
The initiative, dubbed "Project Homecoming", is part of President Donald Trump's sweeping crackdown on illegal immigration, which has also involved detaining hundreds of migrants in a Salvadoran mega-prison.
Immigrants can leave the country on their own, in exchange for free travel and a US$ 1,000 (£749) stipend, and avoid detention or other punishments for being in the US illegally.
The first government-chartered flight took off from Texas and travelled to Honduras and Colombia.
Homeland Security characterised the trip as a "voluntarily charter flight," and not an operation of the US Immigrations and Customs Enforcement (ICE) agency.
Of the 64 individuals on the flight, 38 returned to Honduras and 26 people went to Colombia, the department said.
In March, the Trump administration announced that people in the US illegally could utilise the border patrol app, CPB Home, to depart the country voluntarily. Since then, it has sent some people home on commercial flights.
Officials have described Project Homecoming as a smoother alternative to forcible deportations.
"If you are here illegally, use the CBP Home App to take control of your departure and receive financial support to return home," Homeland Security Secretary Kristi Noem said in a statement.
"If you don't, you will be subjected to fines, arrest, deportation and will never be allowed to return," Noem said.