“It’s a huge disappointment and it’s a big lesson in humility,” said Michel De Wilde, the former senior vice president of research and development at Sanofi Pasteur, who oversaw the vaccine’s development until he left the company in 2013.

The illness, also called breakbone fever, can be excruciating, with high fevers, headaches, muscle and joint pains and lingering weakness. Sometimes the disease causes hemorrhage or shock, which can be fatal.

Some deadly cases have been linked to the fact that there are actually four different types of dengue virus. Research has found that severe illness can occur in people who had one type and later become infected by another. The body’s immune response to the first virus is thought to make the second illness worse, a discovery credited to Dr. Scott B. Halstead, who has been studying dengue since the 1960s.

In February 2016, as the Philippine program was getting underway, Dr. Halstead warned in a scientific article that the vaccine could put people at risk if they had not previously had dengue. He said the issue was well known. “We’ve been talking about this for years,” he said recently. “It isn’t any hidden secret.”

He and others pointed to a trial of Dengvaxia in children, published in 2015, that seemed to confirm fears that the vaccine could be harmful to those with no previous exposure. The potential danger is not from the vaccine itself, but from the immune response to it. The researchers found that in children under 9 years old, those who were given Dengvaxia and later caught dengue were more likely to be hospitalized for severe illness than those who had not been vaccinated.

The finding originally led Sanofi to restrict Dengvaxia to children 9 and older, although the company did not concede that the higher hospitalization rate among younger children was due to their lack of prior dengue exposure. A panel set up by the World Health Organization recommended that the vaccine be used only in places where the incidence of dengue was high.

Brazil decided to limit its government program to people who are over age 15.

Even as Sanofi pushed back against researchers’ warnings about the vaccine’s potential hazards, it ordered another analysis of the data.