Since June, when the first case was reported, there have been 29,704 people infected by the virus, with 204 of them hospitalized, Jorge Melendez told Reuters.
"Having never been in contact with this strain, the Salvadoran population has no defense," Melendez said, adding that nobody has died from the outbreak.
Melendez said most of the cases have been reported in the capital city of San Salvador, where authorities have been cleaning rivers and fumigating.
Infection with the virus, spread by two mosquito species, typically is not fatal but can cause debilitating symptoms including fever, headache and severe joint pain lasting weeks or months. There is no current treatment and no licensed vaccine to prevent it.
The virus showed up for the first time in the Americas late last year. In the United States, locally transmitted infections — as opposed to infections in Americans traveling abroad — have been reported for the first time this year.