The ministry's latest figures show 1,046 of the reported cases have been discarded and the remaining 4,222 cases are still being investigated.
Microcephaly is a rare defect that causes newborns to have unusually small heads and damaged brains.
Before the outbreak, authorities said that on average Brazil had about 150 reported cases a year, though some investigators think the actual number of cases was far greater.
Researchers are trying to determine if Zika is linked to microcephaly, which also can also be caused by factors such as syphilis, rubella or toxoplasmosis.