Fewer than 150 such cases were seen in all of 2014. The Health Ministry has said the surge is linked to Zika virus, a mosquito-borne disease similar to dengue.
The ministry's emergency response official, Wanderson Oliveira, said most of the cases of microcephaly remain concentrated in Brazil's poor northeastern region.
However, the developed southeast where Rio de Janeiro and Sao Paulo are located is the second hardest-hit region. Oliviera spoke at a press conference today.