The health ministry said deaths of infants under the age of one soared by 30 percent in 2016, a year when hospitals and protesters complained of severe shortages of medical supplies.
Deaths of mothers linked to childbirth soared by two-thirds meanwhile, according to the data published by the ministry - the latest such figures since 2015.
It said 11,466 babies died in 2016, up from 8,812 the year before. The report gave no comparative rate in relation to the number of births.
Cases of malaria rose by 76 percent to more than 240,000.
The collapse in prices for Venezuela's crucial oil exports has left it short of cash to import medicine and basic goods.
The Venezuelan Medical Federation says hospitals have only three percent of the medicines and supplies that they need to function normally.
The opposition blames President Nicolas Maduro for the crisis.
Deadly unrest broke out on April 1 as his opponents protested, demanding elections.
Dirty protest
In fresh troubles on Wednesday, police fired tear gas and water cannon at protesters who tried to march to the Supreme Court in Caracas.
Protesters with shields and masks responded by hurling Molotov cocktails, paint bombs and stones.
A 27-year-old man died in the protest in Caracas and another aged 38 died two days after being shot in the head in a protest in the western city of Merida, the state prosecution service said.
Anti-government protesters aim a slingshot during clashes with security forces blocking a march to the Supreme Court in Caracas, May 10, 2017. Source: AAP
That brought the overall death toll from the unrest to 38.
A move by Maduro to reform the constitution has inflamed protesters, who say it is a ploy to resist calls for early elections.
Protesters took to the streets on Wednesday armed with jars of excrement to hurl at police.
"We are using those 'poopootov' bombs as we call them because they repress us with Molotov cocktails, with pellet guns and everything, and this is our only way to throw something at them," one protester told AFP.
'Military trials' concern
Human rights concerns mounted meanwhile as prosecutors challenged alleged plans to try suspects in military courts over the unrest.
Rights groups say scores of people have been brought before military courts after being detained in clashes with police.
The meat shelves are empty at supermarket in severe food shortage in Caracas, March 3, 2015. Source: AAP
Maduro has yet to respond to the reports, which have raised claims he has taken an authoritarian turn in the crisis.
The case challenged on Wednesday involves suspects in the northwestern town of Villa del Rosario de Perija.
Protesters last Friday attacked the town hall and knocked down a statue of late president Hugo Chavez, Maduro's mentor.
State prosecutors requested that 14 people detained over incidents there "be judged by civil and not military courts."
They said in a statement that under the constitution "the people must be tried by regular judges."
A lawyer for rights group Foro Penal, Alfredo Romero, said 73 people were in military custody after being charged with "rebellion."
