Nearly 600 cases of measles, a potentially fatal disease has been recorded in Berlin since October.
An 18-month-old boy died in hospital on 18 February in what is believed the first known fatality in the worst measles outbreak in Germany since 2001.
Berlin's Charite hospital said in a statement that it had treated the measles-infected child which had died and that the cause of death was "still being examined".
Berlin's Health Senator Mario Czaja was quoted in German media as saying the baby had not been immunised against the disease.
It is not clear how the baby boy was infected with measles, said Czaja in a Spiegel Online report.
One school in Berlin was closed after a measles case was confirmed, with staff and students told to bring in vaccination certificates when it re-opens on Tuesday.
Germany had previously set a goal to eradicate measles by 2015, in line with a World Health Organisation target, according to Spiegel Online.
"The outbreak in Berlin is a sobering setback. In general, Germany's immunisation rate is too low," Director Anette Siedler of the Robert Koch Institute, a Berlin-based disease control and prevention organisation, told German media.
There have been calls to introduce compulsory vaccination although national health officials state that there are no plans at present to introduce new legislation.
Germany's Health Minister Hermann Groehe said: "The irrational scaremongering by some of those against vaccinations is irresponsible.
"Whoever denies their child a vaccination is not only putting their child at risk but also others, and this can lead to serious health problems."
Some parents refuse to vaccinate their children because of a theory that the triple vaccine for measles, mumps and rubella (MMR) could cause autism. However this has been repeatedly discredited.
In California, the Department of Public Health reported an outbreak of measles with 123 registered cases recently. Most of those showing symptoms of the disease were not vaccinated.
Germany has a vaccination rate of 95% - one of the highest in the world. Rather than the blame falling on parents, a Deutsche Welle report said that some blame has fallen on visitors and migrants, who have increasingly become the target of campaigns by anti-immigration groups within the country.