The Zika virus has been found in a young man in Sumatra Island in Indonesia, marking the first confirmed case of the disease in the country so far, a research institute says.

Frilasita Aisyah Yudhaputri, the project co-ordinator with the EIJKMAN Institute for Molecular Biology in Jakarta, says they have alerted the country's health authorities to the discovery of the mosquito-borne virus in a 27-year-old man, infected last year.

The man, who was infected with the same strain as that causing alarm in Brazil, had gone to hospital after complaining of a number of ailments, including the sudden onset of a high fever, headache and malaise.

The institute said the man did not exhibit the common clinical characteristics typical of a Zika virus infection, such as a spotted rash and conjunctivitis.

He only showed mild symptoms and recovered within two days.

The institute happened across his case while they were studying a dengue outbreak in the region.

During the period from December 2014 to mid last year, the institute collected samples from more than 100 patients who had been diagnosed with dengue and his happened to come back positive for Zika, the institute's report released on the weekend states.

"The symptoms were very light. But it's still a positive case of Zika among dengue cases. It is the only one that we found so far," Filasita told AAP on Monday.

No other case in Indonesia has been confirmed as yet, she said, but the institute suspects the virus has been in the region for at least a decade.

"The case in 2015 was the first time we had (a confirmed case). (But) from 2007 or even as early as 2000, the trace of it has been suspected," she said.

The institute says the virus can often be misdiagnosed as dengue because it has similar clinical features.