Deaths of mothers in childbirth soared by two thirds meanwhile, according to the data published online by the ministry -- the latest such figures since 2015.
It said 11,466 babies younger than one year old died in 2016, up from 8,812 the year before. The report gave no comparative rate in relation to the number of births.
Among the causes of infant death it cited were septicemia, pneumonia, premature birth and breathing difficulties.
The report said 756 women died in childbirth, just under 66 percent more than the previous year.
Cases of malaria rose by 76 percent to more than 240,000.
Medical associations thought the disease had been eradicated in Venezuela but say it has re-emerged during the past three years of crisis and reached epidemic level in 13 of the country's 24 states.
The collapse in prices for Venezuela's crucial oil exports has left it short of cash to import medicine and basic goods.
Deadly unrest broke out last month with the opposition demanding elections to replace President Nicolas Maduro, whom they blame for the crisis.
Eyewitness? Submit your stories now via social or:
Email: news@pulselive.co.ke
