Lorenzo de Montmollin, head of Argentine naval intelligence, told Brazilian and Chilean officials of the military's plans before deposing Peron, according to the documents.
The coup took place on March 24, 1976, ushering in a seven-year military dictatorship headed by General Jorge Rafael Videla.
The regime kidnapped and killed as many as 30,000 dissidents.
"Montmollin, declaring that he was specifically authorised by the commander in chief of the armed forces to do so, outlined the main steps to be taken by the future regime," Joao Baptista Pinheiro, Brazil's ambassador to Argentina at the time, wrote in a secret telegram dated September 12, 1976.
Pinheiro also transcribed a conversation between a senior Brazilian diplomat and Montmollin in which the Argentine official said Augusto Pinochet, Chile's military leader, had been notified that a coup was being planned.
Pinheiro wrote that the Argentine armed forces asked that Chile abstain from recognising the military government for a while, a request the Chilean authorities agreed to honour.
Montmollin justified the request by indicating that under the Argentine military regime "subversion would be wiped out, but without ostensive violent repression so as to avoid suffering an international campaign like the one that has been unleashed against Chile".
The telegrams also reveal that shortly after the coup, Pinheiro notified the Brazilian government that Argentina and Paraguay had begun co-operating to eliminate left-wing guerrillas.
The programme was the first step in what would eventually become known as Operation Condor.
The military governments of Brazil, Bolivia, Chile and Uruguay also took part in Operation Condor.
Peron went into exile in Spain a few years after the coup. She was arrested by Spanish police in January and could be extradited to Argentina to respond to charges her government was linked to a right-wing death squad.