Brazil’s Foreign Ministry summoned Gabriel Escobar, the highest-ranking US envoy in the capital, on Monday.
The move came after Brazil demanded an explanation from US authorities regarding a "flagrant disregard" for the rights of dozens of deported migrants.
Footage showed several deportees disembarking a civilian aircraft on Friday with their hands cuffed and ankles shackled.
Some deportees claimed they were subjected to physical abuse and denied access to water and bathrooms during the return flight.
The controversy unfolds amid wider tensions in Latin America over US President Donald Trump's strict anti-immigration policies, which include promises to crack down on irregular migration and conduct mass deportations.
However, according to a government source cited by AFP, Friday’s deportation flight was linked to a 2017 bilateral agreement and not to Trump’s recent executive orders.
A related dispute has also escalated between the US and Colombia, which blocked the arrival of US deportation flights over the weekend after migrants were transported on military aircraft.
In response, Trump threatened tariffs and visa restrictions against Colombia.
The two nations avoided a trade clash on Sunday after the White House announced an agreement on deportations and confirmed that no penalties would be imposed.