In a statement issued to IGN's Colin Moriarty, a SCEA spokesperson revealed that "Ueda-san is in fact under contract and is committed to completing his work on The Last Guardian."
This follows a batch of rumours earlier in the month that insinuated the ICO and Shadow Of The Colossus developer had departed Sony, and was completing The Last Guardian in a "freelance" capacity. Earlier this week, The Last Guardian's executive producer Yoshifusa Hayima also departed Team ICO in order to team up with London-based Facebook developer, Bossa.
While the suggestion is that something is "wrong" at Team ICO, we don't necessarily buy into that philosophy. People switch jobs all the time, and The Last Guardian has endured an extraordinarily long development cycle. The bigger concern, as far as we're concerned, is that no-one outside of Sony has seen The Last Guardian in years now.
We'll probably never learn what's really happened at Studio Japan, but if Fumito Ueda does leave Team ICO, we'll be surprised if he finds another publisher willing to give him as much time and freedom as Sony has.