Argentina says Brazil has allowed several RAF flights to operate between Brazilian airports and the Falkland Islands in a breach of agreements between the South American countries.
Argentina lost a brief but bloody war with the UK after Argentine troops invaded the South Atlantic archipelago in 1982.
The Argentine foreign ministry said in a statement that it is "concerned" about six flights last year and 12 in 2015. The ministry said it has requested an explanation from the Brazilian government.
Brazil's foreign ministry said a statement on the matter was being prepared.
Argentina claims the islands it calls Las Malvinas, but the UK says the Falklands are a self-governing entity under its protection.
Argentina reminded Brazil of its commitment "to not allow British airplanes or warships based in the disputed archipelagos" in accordance with agreements among member nations of the regional blocs Mercosur and Unasur.
"The Brazilian foreign ministry reaffirmed its support to our country on this issue and said that it was unaware of these flights," the Argentine statement said.
The war over the islands killed 649 Argentines and 255 UK soldiers.
During her eight years in power, former Argentine president Cristina Fernandez tried to pressure the UK into sovereignty talks by turning away British ships, encouraging companies to divest from Britain and raising other trade barriers.
Tensions have eased since pro-business President Mauricio Macri took office last year promising a less-confrontational stance.
In the biggest breakthrough in decades, the UK and Argentina announced last year that they would work to remove restrictions in the oil, fishing and shipping industries affecting the Falklands.
They also agreed to increase the number of flights between the islands and Argentina.
The Falklands are internally self-governing, but the UK is responsible for defence and foreign affairs.
Argentina claims Britain has illegally occupied the islands since 1833. Britain disputes that and says Argentina is ignoring the wishes of its 3,000 residents who want to remain British.