The materials went missing from a museum being demolished in a special zone around four kilometres (2.5 miles) from the atomic plant in northeast Japan knocked out by a tsunami in 2011.
Although people were allowed to return to the area in 2022 after intense decontamination work, radiation levels can still be above normal and it is surrounded by a no-go zone.
Japan's environment ministry was informed of the theft by workers from a joint venture conducting the demolition work in late July and is "exchanging information with police", ministry official Kei Osada told AFP.
Osada said the metal may have been used in the frame of the building, "which means that it's unlikely that these metals were exposed to high levels of radiation when the nuclear accident occurred".
If radioactivity levels are high, metals from the area must go to an interim storage facility or be properly disposed of. If low, they can be re-used.
However, the stolen scrap metals had not been measured for radiation levels, Osada said.
The Mainichi Shimbun daily, citing unidentified sources, reported on Tuesday that the workers sold the scrap metal to companies outside the zone for about 900,000 yen ($6,000).
It is unclear what volume of metal went missing, where it is now, or if it poses a health risk.
The March 11, 2011, tsunami caused multiple meltdowns at the Fukushima-Daiichi nuclear plant in the world's worst nuclear accident since Chernobyl.
Numerous areas around the plant have been declared safe for residents to return after extensive decontamination work, with just 2.2 percent of the prefecture still covered by no-go orders.
Japan began releasing into the Pacific Ocean last month more than a billion litres of wastewater that had been collected in and around 1,000 steel tanks at the site.
Plant operator TEPCO says the water is safe, a view backed by the UN atomic watchdog, but China has accused Japan of treating the ocean like a "sewer".
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