Hundreds of frustrated and increasingly worried people have been lining up outside medical centres in Sao Paulo over recent weeks in hopes of getting their vaccination -- some getting treated and others to be told that none was available.
Authorities in Brazil's most populous state, with 45 million residents, are trying to make up for the shortfall by distributing partial doses.
The potentially fatal virus, which is transmitted by mosquitoes, is common in Brazil but the scope this year has taken authorities by surprise in Sao Paulo, while tension is also rising in Rio de Janeiro and Minas Gerais states.
Brazilian authorities aim to vaccinate almost 22 million people, according to the World Health Organisation. However, with vaccines in short supply, 16.5 million of them will be given only partial doses.
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Officials say these so-called "fractionated doses" will work for up to eight years, while the full dose lasts a lifetime.
"We are distributing the fractionated doses because of the risk of not having any vaccines," said Marcos Boulos, disease control coordinator for Sao Paulo state.
That doesn't reassure people waiting hours outside vaccination centres or showing up to find signs posted with "No vaccines available."
"We are worried because we haven't managed to get vaccinated," said Maria Pereira, a 33-year-old secretary, who was scouring private clinics in Sao Paulo, where a dose costs about USD 60, rather than free of charge from public providers.
Sao Paulo, which is the biggest city in Latin America, first got the jitters back in October when two monkeys were found dead with the virus in a city park.
In response, the Sao Carlos Ecological Park in Sao Paulo has adopted two orphaned baby monkeys and launched a campaign under the #freemacaco hashtag to appeal for the animals to be protected.
The phenomenon has been repeated in Rio de Janeiro to an even greater extent, with 131 monkeys found dead so far this year, according to the Rio state health secretary -- 69 per cent of them killed by people.
Sao Paulo health authorities have focused vaccination programs on neighbourhoods near the Botanical Garden and zoos, which were all closed a week ago and where monkeys are present.
Where large parts of the population do not have immunity from vaccination, the chances of an epidemic then grow exponentially.
Marcos Boulos, with the Sao Paulo health authorities, says the appearance of yellow fever appearing unexpectedly in city centres is "something not seen before."
However, there is "no indication" that conditions are in place for an urbanisation of the virus, says Barros.