Brazil's Foreign Minister Luis Figueiredo said the interception of Internet data from President Dilma Rousseff reported by US journalist Glenn Greenwald, if proven, "represents an unacceptable and unallowable violation of Brazilian sovereignty."
In Mexico, the foreign ministry said it sent a diplomatic note to Washington calling for an "exhaustive investigation" into claims that the NSA spied on President Enrique Pena Nieto's emails before his election last year.
Mexico warned that, if true, the snooping would be a "violation of international rights" and that it "rejects and condemns any espionage work on Mexican citizens."
Both governments summoned the US ambassadors to their countries, though the envoy to Mexico was out of the country on Monday.
A State Department official sought to downplay concerns, saying that "while we are not going to comment publicly on every specific alleged intelligence activity, as a matter of policy we have made clear that the United States gathers foreign intelligence of the type gathered by all nations."
The claims reported by Greenwald, who obtained secret files from NSA leaker Edward Snowden, follow allegations of widespread US electronic espionage in Latin America that angered the region's leaders.
The report emerged as Rousseff and Pena Nieto, who lead Latin America's two biggest economies, prepare to travel to Russia later this week for a Group of 20 summit during which they will see US President Barack Obama.
Rousseff is also scheduled to visit Washington in October, five months after Obama visited Pena Nieto in Mexico.
Citing a June 2012 NSA document, Greenwald told Globo television on Sunday that the agency was trying to better understand Rousseff's methods of communication and interlocutors using a program to access all Internet content she visited online.
The NSA program allegedly allowed agents to access the entire communications network of the president and her staff, including telephone, Internet and social network exchanges, the Rio-based journalist said.
Figueiredo said he told US Ambassador Thomas Shannon that his government wanted "a formal, written explanation" this week.
After a cabinet meeting with Rousseff, Justice Minister Jose Eduardo Cardozo said Brazil would wait for a response to determine "what measures to take."
The officials said Brazil wants Internet governance and US espionage accusations to be discussed in international forums.
The Brazilian Senate plans to name a special committee on Tuesday to investigate allegations of US spying in the South American country.
Senator Ricardo Ferraco, head of the Senate foreign relations committee, denounced the US government's "lack of limits."
In Mexico, a Mexican diplomatic source said US Ambassador Earl Anthony Wayne was out of the country but was expected in the next hours.
A US embassy source refused to comment on the allegations but said the two countries were in contact and that Obama's visit in May showed both leaders want to "work more closely for the prosperity and security" of their citizens.
The Globo report also said the NSA intercepted some of Pena Nieto's voice mails, which included messages in which he discussed the names of potential cabinet members before his July 2012 election victory.
In July, Greenwald co-wrote articles in O Globo newspaper revealing that the US government had a joint NSA-CIA base in Brazil to gather data on emails and calls flowing through the country.
The issue was discussed during a visit by US Secretary of State John Kerry in August, but Brazil said it was not satisfied by Washington's explanations.
Cardozo, the justice minister, met with US Vice President Joe Biden in Washington last week to discuss the matter and said the United States rejected a Brazilian offer to negotiate a bilateral agreement on surveillance.
Snowden, a former NSA contractor wanted by Washington on espionage charges, is now a fugitive in Russia under temporary asylum.