It was of a variety that normally only comes into flower at the age of eight.
The seeds were sent to the ISS as part of "an educational and cultural project to let children gather the stones and learn how they grow into trees and live on after returning from space," said Miho Tomioka, a spokeswoman for the project's organizer, Japan Manned Space Systems (JAMSS).
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"We had expected the (Ganjoji) tree to blossom about 10 years after planting, when the children come of age," she added.
Kaori Tomita-Yokotani, a researcher at the University of Tsukuba who took part in the project, told AFP she was stumped by the extra-terrestrial mystery.
"We still cannot rule out the possibility that it has been somewhat influenced by its exposure to the space environment," she said.
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Tomita-Yokotani, a plant physiologist, said it was difficult to explain why the temple tree has grown so fast because there was no control group to compare its growth with that of other trees.