Fuel removal was planned to be completed by the end of 2022 and has ended on schedule, JAEA said.
When decommissioning of the plant began in 2018, 160 fuel assemblies were being stored within a sodium-filled storage tank, while 370 fuel assemblies remained within Monju's sodium-filled core.
JAEA began by removing the assemblies from the sodium-filled tank into the water-filled pond, then transferring assemblies from the core into the sodium-filled tank prior to being moved to the storage pond.
JAEA has now announced that the final fuel assembly has been removed from the sodium-filled tank and placed in the water-filled pond.
The 30-year decommissioning plan for Monju, approved by the regulator in 2018, comprises four stages.
Monju, near the Tsuruga nuclear power station in Fukui Prefecture, western Japan, is a 246-MW sodium-cooled fast reactor designed to use mixed fuel rods of uranium and plutonium and to produce more fissile material than it consumes.
It reached criticality for the first time in 1994, but it has mostly been offline since 1995 when 640 kg of liquid sodium leaked from a cooling system, causing a fire.
Monju was allowed to restart in May 2010 after JAEA carried out a review of the plant’s design, and its safety procedures.
However, operation was again suspended in August 2010 after a fuel handling machine was dropped into the reactor during a refuelling outage.
Japan’s government decided to permanently shut down the reactor in 2016.
Decommissioning and dismantling costs are estimated at $3.2bn (€3.26bn), according to earlier reports.