Operator Tokyo Electric Power (TEPCO) is expected to begin the precarious operation later in the day, a tricky but essential step in the plant's decades-long decommissioning plan.
It follows months of setbacks and glitches that have stoked widespread criticism of the utility's handling of the crisis, the worst nuclear accident in a generation.
The work starting today pales in comparison with the much more complex task that awaits engineers, who will have to remove the misshapen cores of three reactors that went into meltdown.
The rods are bundled together in so-called assemblies which must be pulled out of the storage pool where they were being kept when a tsunami smashed into Fukushima in March 2011. There are more than 1,500 such assemblies in the pool.
Over the course of two days, the company said it expects to remove 22 assemblies, with the entire operation scheduled to run for more than a year.
A huge crane with a remotely controlled grabber will be lowered into the pool and hook onto the assemblies, placing them inside a fully immersed cask.
Experts have warned that slip-ups could quickly cause the situation to deteriorate. Even minor mishaps will create considerable delays to the already long and complicated decommissioning.
While such operations are routine at other nuclear plants, the disaster has made conditions far more complex, TEPCO has said.
"This is an important process that is an inevitable part of the decommissioning process, but it includes work that could pose a great risk," the Citizen's Nuclear Information Center, an independent energy think tank, said in a statement.
Hiroaki Koide, assistant professor at Kyoto University's Research Reactor Institute, said the timing of the fuel rod removal was crucial as "the reactor's storage pool is in an unstable condition".
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