Around 880 tonnes of hazardous material are inside the site after a catastrophic tsunami caused by a 9.0-magnitude earthquake triggered one of history's worst nuclear accidents in 2011.
Removing the debris is seen as the most daunting challenge in a decades-long decommissioning project because of the dangerously high radiation levels.
"At 10:03 am (0103 GMT), the second trial extraction operation was started," Fukushima operator Tokyo Electric Power Company (TEPCO) said in a statement.
The second removal comes after TEPCO completed the first trial removal operation using a specially developed extendible device in November.
The sample weighing just below 0.7 grams (0.02 ounces) -- equivalent to about one raisin -- was delivered to a research lab near Tokyo for analysis.
But TEPCO needs more data to examine methods for full-scale debris extractions.
The company said in December it was "upgrading" the telescopic device used for the first experiment by attaching a new camera to its tip.
Three of Fukushima's six reactors went into meltdown in 2011 after the huge tsunami swamped the facility.
Last month, robots began moving sandbags that were used to absorb radiation-contaminated water on underground floors of two buildings at the Fukushima site.
In 2023, Japan began releasing into the Pacific Ocean some of the 540 Olympic swimming pools' worth of treated wastewater, which has been endorsed by the International Atomic Energy Agency.
China banned Japanese seafood imports as a result, and Russia later followed suit.
This month China said it found no abnormalities in seawater and marine life samples that it independently collected near Fukushima in February.
But Beijing indicated that more tests would be needed before it lifts the ban.
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