Sony Worldwide president Shuhei Yoshida told Eurogamer that the game was absent from Sony's E3 presentation because the Tokyo team was working hard addressing technical issues.
"The team is back in Tokyo working hard, and there are some technical difficulties that the team is focused on right now. That's why we don't have an update," Yoshida explained.
The Sony boss denied reports that the game would launch on the PS4, though he was reluctant to say whether or not it would ever see the light of day at all.
"When we have confidence in saying that, we will talk about it. But today, we are working through some engineering effort."
The development status of The Last Guardian was called into question following reports that the game's creator Fumito Ueda was leaving Sony.
The game was subsequently delisted by GameStop, leading to subsequent denials that the game had been cancelled.
> E3 2012: Day One Round-up
The Last Guardian was first revealed in 2009 but has seen a prolonged development with no sign of release.
It was delayed once again last year when Sony announced that it would not make an appearance at the Tokyo Game Show.
Ueda first joined Sony in 1997 and was creative lead on PS2 releases Ico and Shadow of the Colossus.
The two titles have since been remastered as part of the ICO & Shadow of the Colossus Collection on PlayStation 3.
Watch the 2009 Last Guardian trailer below: