It is the first halt for the entire day since all trading at the bourse was computerized in 1999, according to Deutsche press agency (dpa).
The system failure has caused the bourse to suspend all trading since it opened at 9 am (00:00 GMT).
The exchange has a problem in transmitting trading data and also in receiving trading orders, it said in a statement.
The exchange does not know when the system will be restored and offered an apology to investors and concerned parties.
The failure was unlikely caused by a cyber attack, but it was possibly due to an equipment failure, Kyodo News reported, citing exchange officials.
Trading was also halted at the Sapporo, Nagoya and Fukuoka exchanges which use Tokyo's system, the three companies said.
In 2005, a system failure shut down the Tokyo bourse for hours.
