It was a significant step in the decommissioning efforts, but workers still have three heavily crippled reactors to clean up after they were sent into meltdown in the 2011 quake- tsunami disaster.
The overall cleanup work of the Fukushima plant is expected to take decades.
A total of 1,535 fuel rod assemblies have been now taken out of the building after Tokyo Electric Power Co's (TEPCO's) yearlong operation, a company spokesman said.
"Completion of the removal work is a milestone, but the decommission work will continue," plant chief Akira Ono told reporters.
The tsunami battered the plant's cooling system and sent reactors number 1 to 3 into meltdown, setting off the worst atomic accident in a generation.
TEPCO will remove fuel rod assemblies from the pools of other damaged buildings before extracting the melted fuel from the reactors.