The 23 containers arrived in Manila aboard the MV Hansa Augsburg in late September after Indonesian authorities "rejected and reexported" them after discovering traces of radioactive Caesium-137.
Jakarta sent the shipment back as it clamped down on scrap iron and steel imports amid a scandal over alleged radioactive contamination of food products.
A source with knowledge of the situation said the containers were offloaded at Manila's port on Sunday at 10:27 am.
Philippine Nuclear Research Institute (PNRI) director Carlo Arcilla, who called the issue a "solvable problem" in October, told AFP the zinc was now awaiting a medium-term solution, with storage at the Subic Bay military facility a likely option.
He declined to say where the containers were currently located, but another official who spoke on condition of anonymity said they were in a temporary holding area just outside Metro Manila.
"(The Subic Bay Metropolitan Authority) is open to the idea because they have ammunition bunkers there during World War 2. I've seen the bunkers; they are in good shape," Arcilla said, stressing that the contamination levels were low.
"It's weakly contaminated, because one metre (three feet) away from the container, the radiation becomes background," he said, adding that the ship's crew had tested negative for radiation.
The final solution will see the shipment sealed in a purpose-built underground containment facility, he said.
Arcilla went on to say that China's Cosco Shipping Lines, the ship's operator, had been victimised by what he called an "irrational fear of radiation" as well as Manila's failure to find a solution.
"The shipping company took it into their own hands to negotiate because they are losing millions," he said.
Cosco did not immediately respond to questions about the shipment.
Neither the Philippines nor Indonesia have disclosed the radiation levels in the containers.
The zinc dust, a byproduct of steel production, was exported to Indonesia by Zannwann International Trading Corp after being sourced from local recycler Steel Asia, Arcilla said in October.
The recycler temporarily suspended operations at its plant but slammed the PNRI's conclusions as "baseless and unscientific", arguing multiple companies had supplied zinc dust to Zannwann.
Calls to both companies were not immediately returned on Wednesday.
Greenpeace Philippines campaigner Jefferson Chua has warned that even low levels of Caesium-137 exposure carry "long-term cancer risks and can cause lasting environmental contamination".
The radioactive isotope, which is created through nuclear reactions, is used in a variety of industrial, medical and research applications.
pam-cwl/mtp
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