The woman, who works as a tour-bus guide, is the first known person in Japan to test positive twice for the virus amid growing concerns about the outbreak in the country, where more than 180 cases have been confirmed.
Second positive tests have been reported in China, where the disease originated late last year, but this is thought to be the first example outside of the country.
The woman, a resident of Osaka described as being in her 40s, tested positive on Wednesday after she developed a sore throat and chest pains, a statement from the prefectural government said.
She had previously tested positive in late January and was discharged from hospital after recovering from the disease on 1 February, the statement added.
The development came as Tokyo urged large gatherings and sports events to be cancelled or curtailed for two weeks to contain the outbreak, while still pledging that the 2020 Olympic Games would be going ahead in the city.
In addition to the 186 cases reported by Japan’s government, there have also been 704 reported cases on the Diamond Princess cruise ship which was quarantined off Tokyo earlier this month.
Seven people have died so far from the virus, including four people on the cruise ship.
Katsunobu Kato, Japan’s health minister, said the central government would need to review patient lists and check on people who have been previously discharged following the second positive test.
“Once you have the infection, it could remain dormant and with minimal symptoms, and then you can get an exacerbation if it finds its way into the lungs,” Philip Tierno Jr, a professor of microbiology and pathology at NYU School of Medicine, told Reuters.
“I’m not certain that this is not bi-phasic, like anthrax,” Mr Tierno added, meaning the disease could appear to go away before recurring.
The professor also said he believed the Toyko games should be postponed if such conditions continue.
“There are many people who don’t understand how easy it is to spread this infection from one person to another,” he warned.
Toshiro Muto, the CEO of Tokyo 2020, has said officials are considering scaling down the event’s torch relay in an attempt to minimise the potential for the virus to spread.
The government has also said it is considering scaling back this year’s 11 March memorial ceremony for victims of the 2011 earthquake and tsunami which killed nearly 16,000 people.
The coronavirus outbreak has spread rapidly around the world and infected about 80,000 people globally, killing nearly 2,800.
However, the World Health Organisation, which declared a global health emergency in January, resisted making such a declaration at its press briefing on Wednesday.
“The increase in cases outside China has prompted some media and politicians to push for a pandemic to be declared,” Dr Tedros Adhanom Ghebreyesus, the WHO’s director-general, said.
“Using the word pandemic carelessly has no tangible benefit, but it does have significant risk in terms of amplifying unnecessary and unjustified fear and stigma, and paralysing systems.”
He added that the WHO believed the virus had “pandemic potential” but insisted health officials were in a “fight that can be won” to prevent a global crisis.
Additional reporting by Reuters