Tokyo Base was a Federation facility.

In the mid-24th century, Kyle Riker worked out the Fuurinkazan battle strategies at this base. Afterwards, he was asked to come to Starbase Montgomery, where he would work as a tactical advisor to Starfleet, a position he accepted. (TNG: "The Icarus Factor")

According to the Star Trek Encyclopedia (3rd ed., p. 513), Tokyo Base was a Starfleet facility.

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