The IPO-bound exchange 'deeply apologised' for the glitch even as trading went off smoothly at rival BSE where volumes surged.
Sources at the finance ministry said it was a technical problem that led to trading disruptions and there was no information about hacking.
Investors faced problems since morning in executing trade and the exchange stopped trading in cash as well as Futures and Options (F&O) segment.
After at least two attempts to set things right, the National Stock Exchange (NSE) resumed operations at 1230 hours but display issue persisted which was addressed later.
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In a statement issued at around 1530 hours, the exchange said cash market segment did not function normally due to technical problem at the opening today and was closed.
"F&O and CDS (Currency Derivatives Segment) market segments opened normally. Subsequently after giving notice to the market, the F&O segment was also closed," it said.
Despite the chaos, the benchmark 50-share Nifty settled above the 9,700-mark for the first time.
Since morning, investors had faced problems in executing trade and later the exchange stopped trading in cash as well as F&O (Futures & Options) segments.
"We are carrying out an internal review of the technical glitch," he said.
The technical glitch in its trading system also comes at a time when the NSE is awaiting approval from the markets regulator Sebi for its Rs 10,000 crore IPO.
Besides, the watchdog is looking into the issue that the bourse had allegedly provided preferential access to some brokers.
Following the technical glitch, Sebi, in the afternoon, said it was closely monitoring the situation while the finance ministry has sought a report on the matter.
Besides, the matter has been referred to the Standing Committee on Technology to review the problem and approve measures to prevent recurrence of such glitches.
Sources at the finance ministry said this sort of problem faced by the NSE is a serious concern and hoped 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," a source said.
Epic Research CEO Mustafa Nadeem said the problem actually got worse when there was no clear statement or guidance from the NSE about the glitch and the clarification came late at around 1000 hours.