Jesuit Fr. Federico Lombardi, the Vatican spokesperson, made the comments during a briefing Wednesday with reporters in Rome ahead of the trip for World Youth Day.
Lombardi said the Vatican was aware of the agitation that swept through Brazil in June but stressed that the protests "have nothing specifically to do with the pope or the church."
As to whether Francis will address the motives for the June protests, which began in anger over a small increase in bus fares but quickly spread to embraces issues such as poverty, education, health care and perceived corruption, Lombardi said we'll see what Francis has to say when he arrives.
In Brazil, there are indications that the protests could revive while the pope is town -- not out of any opposition to Francis, but taking advantage of the spotlight his presence creates.
Paes conceded that people have the right to protest, but asked them to show understanding.
Organizers of the June uprisings have announced plans to take to the streets again July 26 and 27, while Francis is in Rio de Janeiro, under the banner of, "Pope, look how we are treated!"
Leaders took pains to stress that their protests are not directed at the pope; rather, they're designed to air grievances with what they perceive as substandard public services in Brazil and widespread corruption.
Some 1 million Brazilians took to the streets of major cities during June, and though the rallies were largely peaceful, there were scattered acts of vandalism and violence. At least six people are believed to have died.
Gen. José Elito Carvalho Siqueira, a senior official with the Brazilian security services, said Tuesday that political protests are among other "threats" that could mar the papal visit, including traffic problems, terrorist incidents, and both organized and petty crime.
Siqueira stressed, however, that he believes the police and security services will have adequate personnel deployed to keep things under control.
Brazil's Defense Ministry recently announced it was boosting the number of military personnel assigned to handle security to 10,266 from an initial deployment of 8,500.
Officials in Rio de Janeiro have vowed to stage "the biggest police operation in the city's history," assigning approximately 12,000 regular officers and 1,700 members of an elite security unit.
Siqueira also said security analysts have classified the various events on the pope's itinerary as "green," "orange" or "red," corresponding to the perceived level of risk for disruption.
He said the pope's July 24 visit to the Marian shrine of Aparecida, located roughly 160 miles west of Rio de Janeiro, falls into the "green" category, meaning a low threat level, while most events in Rio for now are labeled "orange."
Organizers of World Youth Day in Rio de Janeiro expect a crowd of around 1.5 million to turn out for a concluding open-air Mass Francis is to celebrate July 28 in Rio de Janeiro.
The trip marks not only his first overseas trip as pope, but also the homecoming of modern history's first Latin American pope.
Aside from the broad-based protests directed at Brazil's political situation, at least two other groups with specific complaints about either the pope or the Catholic church have also announced plans to take to the streets.
A movement called SlutWalk has announced plans for a demonstration July 27 against the church's position on women's issues while a gay rights group has said it will stage a beijaço, in which gay couples exchange kisses and distribute condoms.
Whatever happens, Gilberto Carvalho, the chief of staff to Brazilian President Dilma Rousseff, predicted Francis himself is his own security system.
"The pope will be safe here," Carvalho said, "and not because of the armed forces, but because of ... the sympathy he inspires, since he represents a new hope not just for the church but for mankind."
Lombardi told reporters covering the trip that Francis will stage some sort of session with the media aboard the papal plane en route to Rio de Janeiro, but not in the traditional question-and-answer format, suggesting it would be more of a "getting to know you" exchange than a classic press conference.
He also played down criticism of the costs of the outing, saying the question comes up "on every papal trip." Lombardi said he believes the events are "appreciated and supported" by the majority of people in the host country.
Organizers of World Youth Day have projected a total outlay of $140 million for the event, of which some $60 million is being contributed by the Brazilian government for security, logistics and transport subsidies.
That compares to an estimated $13 billion in public funding Brazil is spending to host the 2014 World Cup.