Two and a half years after the worst nuclear disaster since Chernobyl, the operator of Japan's wrecked Fukushima plant faces a daunting array of unknowns.

Why the plant intermittently emits steam; how groundwater seeps into its basement; whether fixes to the cooling system will hold; how nearby groundwater is contaminated by radioactive matter; how toxic water ends up in the sea and how to contain water that could overwhelm the facility's storage tanks.

What is clear, say critics, is that Tokyo Electric Power is keeping a nervous Japanese public in the dark about what it does know. The inability of the utility, known as Tepco, to get to grips with the situation raises questions over whether it can successfully decommission the Fukushima Daiichi plant, say industry experts and analysts.

(Read more: Tepco: Fukushima likely leaking radioactive water into sea)

"They let people know about the good things and hide the bad things. This culture of cover up hasn't changed since the disaster," said Atsushi Kasai, a former researcher at the Japan Atomic Energy Research Institute.

Tepco's handling of the clean-up has complicated Japan's efforts to restart its 50 nuclear power plants, almost all of which have been idled since the disaster over local community concerns about safety.

That has made Japan dependent on expensive imported fuels for virtually all its energy.

Radiation complicates the job

A 9.0 magnitude earthquake and subsequent tsunami off Japan's eastern coast killed nearly 20,000 people on March 11, 2011. It also destroyed the Fukushima plant, causing meltdowns at some of its reactors and hydrogen explosions. Radiation leaked into the air and sea.

Tepco was heavily criticised by nuclear experts and the government at the time for what was seen as an inept response to the disaster. It has won few supporters since.

The company says it is doing its best with the clean-up at the plant, 200 kilometers (125 miles) northeast of Tokyo, adding so much is unknown because workers cannot get to every corner of the facility because of high radiation. But the missteps continue.

(Read more: Suspected new leak found at Japan's crippled Fukushima nuclear plant)

Reversing months of denials, Tepco said on July 22 that radioactive water from the plant was reaching the ocean.

That was the latest, and according to experts and anti-nuclear activists, the most glaring in a string of belated admissions that have undermined public trust in Japan's largest utility.

In January, Tepco found fish contaminated with high levels of radiation inside a port at the plant. Local fishermen and independent researchers had already suspected a leak of radioactive water, but Tepco denied the claims.

It investigated only after Japan's new nuclear watchdog expressed alarm earlier this month at Tepco's own reports of huge spikes in radioactive cesium, tritium and strontium in groundwater near the shore. Tepco apologized while President Naomi Hirose took a pay cut as a result.

"They had said it wouldn't reach the ocean, that they didn't have the data to show that it was going into the ocean," said Masashi Goto, a former nuclear engineer for Toshiba who has worked at plants run by Tepco and other utilities.

Frustrated at communication

A Tepco spokesman said the company was trying to communicate with the public.

"We do our best to present our explanations behind the possible causes of what's happening," he said.

Tepco was incompetent rather than intentionally withholding information, said Dale Klein, who chairs a third-party panel commissioned by Tepco to oversee the reform of its nuclear division and a decommissioning process that could cost at least $11 billion and take up to 40 years.

"The plant is in a difficult physical configuration. I have some sympathy," Klein, a former chairman of the U.S. Nuclear Regulatory Commission, told Reuters.

"It's not the fact that we're having surprises - it's the way they're handling them. That's where my frustrations are."

Tepco says it is dealing with the clean-up hand-in-hand with the government. It has also relied on expertise from the U.S. Department of Energy and General Electric.

But a Reuters investigation in December found that foreign companies had won few, if any, contracts to develop technologies for scrapping the reactors.

(Read more: Japan's anti-nuclear protest two years after Fukushima)

Tepco, accused by experts of lacking transparency even before the disaster, was heavily criticized in the days after the calamity for not providing timely information to the public.

It was more than two months before it said three of the six reactors at the plant had suffered nuclear meltdowns. Industry experts had suspected meltdowns long before that.

Since the beginning of this year, the plant has been plagued by problems.

A worker on the site spotted steam rising from the No. 3 reactor building, but Tepco has only been able to speculate on its cause. In March, a rat shorted a temporary switchboard and cut power for 29 hours that was used to cool spent uranium fuel rods in pools.

Water storage nightmare

Experts say Tepco is attempting the most ambitious nuclear clean-up in history, even greater than the Chernobyl disaster in 1986.

One of its biggest headaches is trying to contain radioactive water that cools the reactors as it mixes with some 400 tons of fresh groundwater pouring into the plant daily.

Workers have built more than 1,000 tanks to store the mixed water, which accumulates at the rate of an Olympic swimming pool each week.

With more than 85 percent of the 380,000 tons of storage capacity filled, Tepco has said it could run out of space.

The tanks are built from parts of disassembled old containers brought from defunct factories and put together with new parts, workers from the plant told Reuters. They say steel bolts in the tanks will corrode in a few years.

Tepco says it does not know how long the tanks will hold. It reckons it would need to more than double the current capacity over the next three years to contain all the water. It has no plan for after that.

(Read more: Two years after Fukushima, Japan's nuclear lobby bounces back)

Instead, the utility wants to stem the flow of groundwater before it reaches the reactors by channeling it around the plant and into the sea through a "bypass".

The groundwater would be captured at the elevated end of the plant into a system of wells and channeled into pipes that would carry it to the sea.

Local fishermen oppose the idea, dismissing Tepco's claims that radiation levels in the water would be negligible.

Meanwhile, Tepco's improvised efforts to stop radioactive water leaking into the sea include sinking an 800-meter-long steel barrier along the coastline, injecting the ground with solidifying chemicals and possibly even freezing the ground with technology used in subway-tunnel construction. Industry experts are not impressed.

"You can't do temporary fixes in nuclear power," said Goto. "They say everything's fine until bad data comes out."