Considered one of the largest public sector banks with 3,000 branches nationwide, the glitch "largely affected" transactions, hampering day-to-day operations, they said.
IOB Chairman and Managing Director M Narendra said services were affected on Monday and restored on Tuesday.
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However, for the fourth day today, banking as well as ATM services continued to remain affected.
A senior IOB official told PTI that "the issue was sorted out and system is working today".
The bank had registered 8.95% increase in total business for the quarter ending June 30, 2013 at Rs 3,63,087 crore, compared to Rs 3,33,250 crore during the corresponding period of previous year.
The bank has about 2,000 ATM networks across the country.