There have been 3,893 cases of microcephaly since October, when the authorities first noticed a surge, up from 3,500 in last week's report.
Zika is transmitted by the bite of the Aedes aegypti mosquito, which also spreads dengue and chikungunya.
Brazil is experiencing the largest known outbreak of Zika.
The Zika virus has already killed five babies in the country, said the Health Ministry. Another 44 cases are being investigated.
Last week, Health Minister Marcelo Castro said a new testing kit was being developed to identify quickly the presence of either of the three viruses.
He also announced extra funds to speed the development of a vaccine for Zika "in record time". Read more on bbc.