"Currently, we plan to reopen on March 16. But we'll decide when to open by looking at the situation and developments. We'll also consult (official) agencies concerned," a spokesman told AFP.
More than 30 million visitors flood into the two parks per year, and they are among the most popular destinations for tourists coming to Tokyo.
The move comes as the Japanese government steps up measures to tackle the outbreak of the virus, which has been linked to at least four deaths in the country and nearly 200 infections.
On Thursday night, Prime Minister Shinzo Abe urged schools across the country to close for around a month, though nurseries and after-school clubs are exempt.
And the government has urged people to work from home and commute during off-peak hours, as well as avoid large gatherings.