The exchange announced the shutdown at 9 am local time, adding later that all trading would be halted for the entire day.
TSE operator, Japan Exchange Group, has released a statement saying the issue will be fixed in time for trading on Friday.
Japan Exchange Group blames the shutdown on unspecified hardware responsible for relaying market information. When that equipment failed, a backup failed to take its place.
The outage is the first to affect all listed stocks on the TSE since 2005. Exchanges in Nagoya, Fukuoka, and Sapporo were also affected by the downtime.