HICKSVILLE, N.Y.  — Two weeks after Superstorm Sandy, while most utilities have restored electricity to nearly all their customers, there was one glaring exception Monday: a Long Island power company with more outages — almost 60,000 Monday — than all the others combined.

As people on Long Island fumed over the cold and the darkness and complained that they couldn’t get answers from the company, the Long Island Power Authority said in its defense that the storm was worse than anyone could have imagined, and that it didn’t just damage outdoor electrical lines; it caused flooding that touched home and business breaker boxes.

LIPA also acknowledged that an outdated computer system for keeping customers notified has added to people’s frustration.

But some say the government-run utility should have seen it coming. It was recently criticized in a withering state report for lax preparation ahead of last year’s Tropical Storm Irene and for the 25-year-old computer system used to pinpoint outages and update customers.

“It’s antiquated. I think they’re negligent,” said Phil Glickman, a retired Wall Street executive from South Bellmore who waited 11 days to get electricity back.

LIPA has restored power to nearly 1.1 million homes and offices all together. About 46,000 still waiting for the lights to come back on are along Long Island’s south shore and Rockaway Peninsula and had water damage to electrical panels and wiring, so their service can’t be restored without an inspection and possibly repairs. The utility said it expects to restore service to the last 11,000 customers outside flooded areas by late Tuesday or early Wednesday.

At its peak, the storm knocked out power to 8.5 million customers in 10 states, with New York and New Jersey bearing the brunt. Those outages have been nearly erased, though Consolidated Edison, the chief utility in New York City, has cited problems similar to LIPA’s, saying about 16,300 customers in flooded areas of Brooklyn, Queens and Staten Island can’t get service until their internal electrical equipment is repaired, tested and certified.

LIPA customer Priscilla Niemiera, whose finished basement in Seaford flooded, said her house needs to be inspected and she can’t get any answers. Every time she calls the utility, she said, she gets hung up on.

“I think LIPA should be broken up into small companies and it shouldn’t be a monopoly anymore because this is every single time we have a disaster. And then they raise the rates. We’re paying very high rates. We’re paying high taxes, high electric. Everything,” she said.

LIPA, whose board is chosen by the governor and lawmakers, contracts with National Grid for service and maintenance. Last year, its board chose a new contractor, New Jersey’s Public Service Enterprise Group, which will take over in 2014. Gov. Andrew Cuomo criticized the storm response of all New York utilities in the region, saying their management had failed consumers.

A state report criticized LIPA in June for poor customer communications after Irene last year and for insufficient tree trimming. The Department of Public Service noted major problems in telling customers estimated power-restoration times, faulting its computer system, which a consultant had found deficient back in 2006.

LIPA acknowledged that customers aren’t getting the information they need, partly because of the system, which it is updating. Authority officials said the new system will be operating next year.

“It is a huge computer system. After Irene we immediately accelerated that process, and even at that it is still an 18-month to two-year process,” LIPA’s chief operating officer, Michael Hervey, said Monday. “We would have liked to have had it up and running for now, but it’s just such a large magnitude computer system that it takes that long.”

Hervey said the company will be working with remaining customers over the next several weeks as they get their homes repaired. “They can’t be safely re-energized from an electrical standpoint,” he said. “We are ready to service those areas, but they are not ready to take it right now.”

John Bruckner, president of National Grid Long Island transmission and distribution, said he had about 15,000 people working on restoration, including 6,400 linemen from all over the U.S. and Canada.

Matthew Cordaro, co-chairman of the Suffolk Legislature’s LIPA Oversight Committee and a former utility executive, said Con Ed and Public Service Electric & Gas New Jersey did a good job responding to the storm, and LIPA didn’t.

While a storm of that magnitude would challenge any electricity provider, he said LIPA is probably one of the most poorly run utilities and has a “crazy” public-private organizational structure that’s fraught with problems and raises questions of accountability.