In absolute terms, the risk is low in all Cup venues, but comparatively greater in the three northeastern cities and authorities should beef up steps to prevent an outbreak, they said.
A potentially dangerous fever caused by a virus for which there is no vaccine or cure, dengue is transmitted by the Aedes aegypti mosquito when it takes a blood meal.
Doctors last year sounded the alarm over dengue at the June 12-July 13 tournament. The disease is endemic in Brazil, which is expected to lure hundreds of thousands of football visitors.
Writing in the journal The Lancet Infectious Diseases, a team of European and Brazilian experts crunched the numbers to pinpoint areas of risk.
They looked at real-time weather patterns provided by four meteorological agencies, particular rainfall which affects mosquito breeding.
They matched these against 13 years of data from prior dengue outbreaks in the month of June in 553 "microregions" of Brazil, including the 12 tournament host cities.
The researchers factored in the dynamics of how a dengue outbreak builds up.
It takes between seven and 14 days for a mosquito to become infectious with the virus it has picked up from a human. And when the insect bites another human, the virus needs four to seven days to incubate.
Visitors are not expected to stay in the same city for more than two or three weeks, which means an epidemic must already be well underway for large numbers to be vulnerable in June.
- Calculating the risk -
"Our forecasts for June 2014 showed that dengue risk was likely to be low in the host cities Brasilia, Cuiaba, Curitiba, Porto Alegre and Sao Paulo," wrote the team.
"The risk was medium in Rio de Janeiro, Belo Horizonte, Salvador and Manaus. High-risk alerts were triggered (in the study) for the northeastern cities of Recife, Fortaleza and Natal."
It added: "efforts to reduce dengue incidence and severity should be concentrated in these cities."
Potential measures include attacking mosquito breeding sites in stagnant pools of water and rubbish.
"The risk is more likely to be low in all 12 host venues," lead author Rachel Lowe from the Catalan Institute of Climate Sciences in Barcelona, Spain, told AFP by email.
The three northeastern cities and Manaus are considered to be comparatively more at risk because the Amazon region had heavier-than-usual rainfall in the 2013-14 southern hemisphere summer.
The south and southeast of the country had an atypically hot and dry summer, which reduced mosquito infestation in Porto Alegre, Curitiba and Sao Paulo.
Dengue incidence rates are considered "high" by the Brazilian ministry of health when they exceed 300 cases per 100,000 inhabitants, said Lowe.
The team added a large margin (18 percent) to this threshold for their World Cup forecast, given that short-range predictions can be prone to greater error, she explained.
Fortaleza and Natal had a higher probability than Recife of exceeding the benchmark.
About 80 percent of people infected with the dengue virus develop no symptoms, but about five percent develop severe illness and for a further one percent, it is life-threatening.
So far this century, Brazil has recorded more cases of dengue than any other country in the world, with more than seven million cases between 2000 and 2013, the study said.