Argentina has accused the US of trying to smuggle weapons and satellite phones into the country after cargo on a US military plane was seized last week.
Argentine officials say the material was not properly declared.
The US says the equipment was intended for a police training course in Argentina and has demanded its return.
Bilateral ties have cooled since it emerged US President Barack Obama would not be visiting Argentina during a forthcoming tour of the region.
Argentine Foreign Minister Hector Timerman on Monday sent a formal protest to the US embassy, demanding a proper explanation about the seized cargo.
"The United States must understand that they can't send war materials without informing the government. And now they refuse to co-operate with the investigation," Mr Timerman told CNN.
The Argentine government said that the material seized at Ezeiza International Airport last Thursday included weapons, satellite communications equipment and medicine such as morphine.
But US state department spokesman PJ Crowley said they were "puzzled and disturbed" by the actions of Argentine officials, who had conducted an "unusual and unannounced" search of the aircraft.
Mr Crowley said he had heard that one serial number had not been documented properly, an issue that could have easily been resolved.
"For whatever reason, it was elevated to higher levels of the government and we find this puzzling," he said.
He said the US was calling for its equipment to be returned. The training course which involved US military experts and Argentine federal police and focussed on hostage rescue techniques had been cancelled, he added.
President Obama is set to visit El Salvador, Brazil and Chile during a visit to Latin America next month.
Reacting to the news that Argentina was not on the itinerary, Mr Timerman said that the US had "more interests than friends".
He said bilateral ties were excellent in some spheres, while there were differences in others.