A total of 7,936 suspected cases of microcephaly were reported in the past nine months, 3,308 of which have been dismissed of its link to the virus and 3,047 remain under probe.
According to the ministry, the cases are registered in all but one northern state – Acre -Brazil.
The ministry also confirmed 317 deaths of newborns since October as a result of microcephaly.
Microcephaly is a birth defect marked by unusually small heads and underdeveloped brains.
The ministry added that it could be caused by a number of factors such as drug use during pregnancy and rubella.
It said the sudden rise in microcephaly cases in Brazil since 2015 had been mainly attributed to the mothers’ exposure to the Zika virus.
Zika is raging across Latin America, with Brazil having registered the largest number of microcephaly cases.
The country’s northeastern states have been hardest hit, especially Pernambuco (336 cases), Bahia (254) and Paraiba (139).
The spike in birth defects prompted the government to declare a health emergency at the end of 2015 and to take measures to curb reproduction of mosquitoes that transmit the virus.
On Tuesday, the World Health Organisation (WHO), reported an observed increase in neurological disorders and neonatal malformations due to Zika.
WHO maintained its previous advice against restrictions on travel and trade, with countries affected by the epidemic, including the cities in Brazil that would be hosting the Olympic and Paralympic Games.
However, the WHO counseled pregnant women to avoid travelling to areas with ongoing Zika outbreaks, and to practice safe sex during their pregnancy if their partners live in or traveled to the affected areas.