Government officials confirmed a single case of the mosquito-borne Zika virus had been detected in Jambi on Sumatra island. It was discovered by researchers studying specimens taken during a dengue fever outbreak between December 2014 and April 2015.
"We found an infected patient in Jambi. The presentation by the health minister showed that it is under control," senior minister Puan Maharani told reporters after a high-level meeting convened by President Joko Widodo to discuss the virus.
Health experts have warned Asia is particularly vulnerable to the virus, given that the Aedes aegypti mosquito - which carries Zika, dengue fever and the chikungunya virus - thrives in its congested cities.
Officials in Indonesia, a tropical country of 250 million where urban outbreaks of mosquito-borne illnesses are common, called for calm and vigilance.
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"People must not panic and continue to keep their surroundings clean," said Maharani.
"The government is ready to anticipate this so it does not become an epidemic in Indonesia."
The case was detected by chance as researchers examined specimens from a dengue fever outbreak, and concluded that the Zika virus had likely been circulating in Indonesia "for a while".
The World Health Organization has warned that the virus is "spreading explosively" in the Americas, with three million to four million cases expected this year.