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Most of the workers were asymptomatic and self-isolating at home, said Badai Ismoyo, head of the health office in the district of Kudus in central Java, but dozens have been hospitalized with high fevers and falling oxygen-saturation levels.
Designated as a priority group, healthcare workers were among the first to be vaccinated when inoculations began in January.
Almost all have received the Covid-19 vaccine developed by Chinese biopharmaceutical company Sinovac, according to the Indonesian Medical Association (IDI).
While the number of Indonesian healthcare workers dying from Covid-19 has dropped sharply from 158 in January to 13 in May, according to data initiative group LaporCovid-19, public health experts say the Java hospitalizations are cause for concern.
A spokesperson from Sinovac was not immediately available for comment on the efficacy of the Chinese firm's CoronaVac against newer variants of the virus.
As Indonesia grappled with one of Asia's worst outbreaks, with over 1.9 million infections and 53,000 deaths, its doctors and nurses have suffered a heavy toll of 946 deaths.
Many are now experiencing pandemic fatigue and taking a less vigilant approach to health protocols after being vaccinated, said Lenny Ekawati from LaporCovid-19.
Across Indonesia, at least five doctors and one nurse have died from Covid-19 despite being vaccinated, according to LaporCovid-19, although one had only received a first shot.
Siti Nadia Tarmizi, a senior health ministry official, did not immediately respond to a request for comment on how many doctors have died since the vaccination program began.
In Kudus, one senior doctor has died, said IDI.
Nadia said there had been no deaths in Kudus since a new outbreak began in the past several weeks among medical workers and that those who contracted Covid-19 have had mild symptoms.
In Jakarta, the capital, radiologist Dr Prijo Sidipratomo told Reuters he knew of at least half a dozen doctors hospitalized with Covid-19 in the past month despite being vaccinated, with one now being treated in an ICU.
"It is alarming for us because we cannot rely on vaccinations only," he said, urging people to take precautions.
Weeks after the Muslim Eid Al-Fitr holidays, Indonesia has experienced a surge in cases, with the positivity rate exceeding 23% on Wednesday and daily cases nearing 10,000, its highest since late February.
In its latest report, the WHO urged Indonesia to tighten its lockdown amid increased transmission and a surge in bed occupancy rates.