Sources at the ministry said it was a technical problem that led to trading disruptions and there was no information about hacking.
Investors faced problems on the NSE, which had briefly stopped trading in cash and F&O (futures and options) segments. Later, trading activities resumed at 1230 hours.
Sources said Sebi is constantly monitoring the situation and this sort of problem is a serious concern for the ministry, hoping that such situations do not happen again.
"Let's wait for the report. The NSE will send a detailed report to Sebi. The report will be sent to us through Sebi. We expect an interim report from Sebi by the end of the day," the sources said.
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In a statement, the Securities and Exchange Board of India (Sebi) said it is in touch with the NSE and is closely monitoring the situation.
The NSE is the largest stock exchange in India in terms of total and average daily turnover for shares every year since 1995, as per Sebi data.
A BSE spokesperson said the exchange is not facing any problems.