Some 200,000 people turned out to celebrate the Pope's first mass in Cuba but not all were welcome.
More than 150 anti-government protesters have reportedly been arrested. Demonstrators hope Benedict's historic visit will boost human rights.
But the Vatican's spokesman has refused to be drawn on the subject.
He did, however, say that "people have the right to protest but at the same time people have a right not to be disturbed during their religious activities."
Although the Vatican is not publicly saying so, it is widely understood that this trip is aimed at cementing relations between the Catholic Church and the communist state.
With Cuba undergoing radical political and social changes, the Church hopes Benedict's presence will also help spark a faith revival.
President Raul Castro has steadily improved ties with the Church, using it as a mediator on issues such as political prisoners.
But Vatican officials say Benedict's schedule does not allow meetings with dissidents, who claim Castro's government is trying to silence them.