Brazil was outraged after media reports of widespread US phone and Internet eavesdropping based on information leaked by fugitive intelligence contractor Edward Snowden.
Foreign Minister Antonio Patriota told a press conference after talks with Kerry that revelations about the vast US global surveillance network posed a "new challenge in our bilateral relationship."
"If the implications of this challenge are not satisfactorily resolved, they run the risk of casting a shadow of mistrust over our work," he added in Brasilia.
"Practices which harm the sovereignty and relations of trust between states and violate the individual freedoms which our countries so cherish must be stopped," Patriota said.
Kerry, who is on his first trip to South America since he assumed his post in February, said: "Brazil is owed answers with respect to those questions and they will get them."
"We will have this dialogue with the view to make it certain that your government is in complete understanding and complete agreement with what it is that we must to do provide security, not just for Americans, but for Brazilians and the people of the world," Kerry added.
US officials have defended the vast telephone and Internet surveillance programs as essential to foiling worldwide terrorist attacks.
Brazil, Latin America's economic powerhouse, has meanwhile sought to assert regional independence from Washington.
Kerry arrived here late Monday from Colombia, where he also defended Washington's electronic espionage in the region.
"I think it's very obvious to everybody that this is a dangerous world we're living in," Kerry told reporters in Bogota on Monday, referring to the September 11, 2001 terrorist attacks.
"And we are necessarily engaged in a very complex effort to prevent terrorists from taking innocent lives in many different places," he added.
Based on documents leaked by Snowden, the daily O Globo reported last month that Washington eavesdropped on Brazilians' phone calls and Internet communications.
A spy base in Brasilia, part of a worldwide network of 16 such stations operated by the US National Security Agency, also intercepted foreign satellite transmissions, it claimed.
O Globo also published an NSA document which seemed to indicate that the Brazilian embassy in Washington and the Brazilian mission to the UN in New York were targeted by the US spy agency.
Snowden, who was granted asylum in Russia on August 1 after spending over five weeks in a Moscow airport transit zone, is said to now be at an undisclosed location in the country.
The United States wants to put him on trial for leaking sensitive US secrets but Moscow has steadfastly refused to hand him over.
Kerry and Patriota also discussed Brazilian President Dilma Rousseff's scheduled state visit to the United States in October.
Last week, Patriota insisted that despite the furor over US snooping in Brazil and several other Latin American countries, the trip was still on.
Kerry was scheduled to meet Rousseff later in the day.
Over the past five years, US-Brazilian trade grew by 11.3 percent from $53.1 billion to $59.1 billion, making the United States Brazil's second largest trading partner after China.
In 2012, the United States was also the biggest foreign investor in Brazil.
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