Gazing down at the glassy surface of the spent fuel pool inside the No 4 reactor building at Fukushima Daiichi, it is easy to underestimate the danger posed by the highly toxic contents of its murky depths.

But this lofty, isolated corner of the wrecked nuclear power plant is now the focus of global attention as Japan enters the most critical stage yet in its attempt to clean up after the worst nuclear accident in the country's history.

Later this month the plant's operator, Tokyo Electric Power (Tepco), will begin removing more than 1,500 fuel assemblies from the pool, the first step in a decommissioning process expected to last at least three decades.

On Thursday, the Guardian witnessed Tepco's preparations for an unprecedented operation that the utility's critics claim has the potential to end in disaster.

The risk posed to the reactor by earthquakes and other natural catastrophes has made removal of the fuel – 1,331 spent assemblies and 202 fresh ones – a matter of urgency. An event similar to the 9.0 magnitude quake that crippled the plant on 11 March 2011 could collapse the fuel pool altogether, some observers say, leading to the leaking of huge quantities of radiation into the atmosphere. Tepco, however, insists the structure could withstand such a quake.

Reactor No 4 had been shut down for maintenance checks when the quake and subsequent tsunami struck, but a hydrogen explosion days later blew off its roof and exposed the fuel pool, located 100 feet above ground, to the elements.

In the 32 months since the disaster, workers have reinforced the reactor building and covered it with a huge steel canopy. Tepco officials conceded, however, that the fuel removal carries significant risks, particularly if the assemblies collide or are exposed.

"If, for some reason, the water levels dropped, the fuel would quickly heat up," said Takashi Hara, a Tepco employee in charge of fuel removal.

There are fears, too, that some of the uranium pellets inside the fuel rods may have been damaged, although Tepco says it has found no evidence of this.

The man who will oversee the delicate operation played down fears of a major accident. "The potential for another disaster is very close to impossible," said the plant's chief, Akira Ono. "Removing spent fuel is done at any ordinary nuclear power plant, and the equipment and methods we'll be using here are not that different."

Yet what is considered routine at other nuclear plants represents uncharted territory at Fukushima Daiichi.

A newly built crane that will manoeuvre the fuel must be operated manually, rather than automatically, because the assemblies are not exactly where they should be; and the pool is still littered with tiny pieces of debris caused by the blast.

Each batch of fuel rods will be placed into dry casks, which will then be lowered to ground level and transported to a safer storage site nearby.

Tepco says work could begin as early as next week, adding that it hopes to complete the task by the end of next year.

The risks prompted the head of Japan's nuclear regulator, Shunichi Tanaka, to call on Tepco to exercise extreme caution. "The process involves a very large risk potential," he reportedly told the firm's president, Naomi Hirose. "In a sense, it is more risky than the radioactive water crisis."

Some nuclear experts say Tepco, still reeling from international criticism of its inability to stem massive leaks of contaminated water into the Pacific ocean, is deliberately playing down the risks.

"A task like this has never been done before, and obviously it is extremely dangerous," said Charles Perrow, an emeritus professor at Yale University.

"I would be reassured if experts from other nations were allowed to inspect the site, make recommendations and observe the process. Or better yet, do the work. Rather than damage the nation's pride, it would increase other nations' confidence in the ability of Tepco to handle the job."

Shaun Burnie, a nuclear consultant, said Tepco had "clearly demonstrated its inability" to manage the cleanup.

"Does that mean they cannot be trusted to remove the fuel from Fukushima?" he asked. "That's irrelevant. They are going to remove the fuel and therefore the question is whether their plan is the best option without risk.

"They have to remove the fuel as early as possible – the risk from major structural failure leading to pool collapse is a greater threat than leaving the fuel in situ.

"The probability that the operation will go wrong in some way given the unique challenges and Tepco's track record must be considered a real risk."

But Dale Klein, former chairman of the US nuclear regulatory commission and chair of Tepco's nuclear reform monitoring committee, said the removal of the spent fuel would be "a milestone".

"The engineers were very creative in building a new fuel-handling device for the spent fuel in No 4 pool," Klein said.

Fuel removal is not the only challenge facing the 6,000 workers battling to make Fukushima Daiichi safe. Large areas of the plant are still a chaotic network of pipes and cables – reminders that this was the world's worst nuclear crisis in over a quarter of a century.

The pipes carry water from the damaged reactors to a hanger-like decontamination facility, where dozens of radionuclides, including caesium, are removed. The 860-acre site is now home to more than 1,000 storage tanks, holding a combined 350,000 tons of contaminated water. Wooded areas are being cleared to make room for more tanks.

Near the coastline, the rusty, mangled remains of vehicles swept up by the tsunami have been left exactly where the waves dumped them, while workers focus instead on bolstering the plant's defences against a possible future tsunami and trying to stem leaks of toxic water into the Pacific ocean.

Even if all goes to plan, Tepco officials concede that securing reactor No 4 is only a first step: work to remove molten fuel from three neighbouring reactors that suffered meltdown won't begin for at least another six years.

Radiation levels in those reactors are still too high for humans to enter, and attempts to use robots to determine the exact location of the melted fuel have failed. Instead, officials are placing their faith in the law of gravity, assuming only that the highly hazardous material lies somewhere deep inside the reactor basements.

Given the potential dangers ahead, handling spent fuel rods could prove the least of Japan's nuclear worries.