Between January 3 and April 2, 91,387 suspected cases of Zika were reported, with a disproportionate share (30,286) in the poorer northeast of the country, the Health Ministry said.
Three people have died of the mosquito-borne virus, it said.
Despite a flurry of research, very little is known about the virus -- how long it can hide out in the human body, the degree of risk via sexual transmission, the full list of diseases and disorders it may cause, and all the mosquito types capable of transmitting it.
Recent scientific consensus is that Zika causes microcephaly, a form of severe brain damage in newborns, and adult-onset neurological problems such as Guillain-Barre Syndrome, which can cause paralysis and death.
There is no vaccine or treatment for the virus, which in most people causes only mild symptoms -- a rash, joint pain or fever.
Among the infected to date have been 2,844 pregnant women.
"So far, it is not possible to determine what percent of Zika-positive pregnant women may have babies with microcephaly," said Infectious Disease Monitoring director Claudio Maierovitch.
Meanwhile, dengue cases surged to 802,429 -- 13.7 percent more than in the same period a year earlier, government data showed.