The 18-month-old boy died on February 18, the first known fatality among more than 570 recorded measles cases since October in the German capital, a Berlin health department official told AFP.
The resurgence of the preventable disease in Germany, as well as in parts of the United States, coincides with a movement among some parents to refuse to vaccinate their children.
Health Minister Hermann Groehe said "the irrational fear-mongering of some vaccination-foes is irresponsible".
"Those who refuse to vaccinate their children endanger not only them but others, threatening serious health problems."
But they said the government would ensure that parents receive advice on the need for immunisations when children start early child care.
Vaccination certificates would also be checked during regular doctors visits, a health ministry spokeswoman said.
She added that "if that doesn't help, other steps will have to be considered."
Berlin's prestigious Charite hospital said later in a short statement that it had treated the measles-infected child which had died and that the cause of death was "still being examined".
Many foes of immunisation
The centre for diseases control and prevention, the Robert Koch Institute, said the Berlin wave of infections had "initially affected primarily asylum seekers, mostly from Bosnia and Herzegovina and Serbia"."But now cases of the disease are occurring primarily amid the general population of Berlin," it said in a statement.
Measles causes fever and rash and in severe cases can lead to pneumonia or brain swelling, sometimes fatal. The disease is highly contagious because it is transmitted through the air.
Many people who do not vaccinate their children say they fear a triple vaccine for measles, mumps and rubella is responsible for increasing cases of autism - a theory repeatedly disproven by various studies.
The controversy dates back to the publication of a now debunked article in the Lancet medical journal in 1998.
Some parents also refuse vaccination on religious or political grounds.
Berlin health ministry chief Mario Czaja said the infant's death confirmed that measles is a serious disease.
"There are many foes of immunisation who dismiss measles as a childhood disease," he was quoted as saying by national news agency DPA.
Czaja urged adults to check whether they had received a measles jab, saying the immunisation rate amid children in Berlin stood at 95 per cent.
One high school stayed closed in Berlin Monday following a measles case.
Students and staff were asked to bring proof when it reopens Tuesday that they had been vaccinated against measles.
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