Stewart is battling to overcome a damaged medial ligament and ran for the first time on Thursday in front of the team's medical staff at Kogarah Oval.
The Manly back-rower will be given until Friday to prove his fitness, with the team flying north to Queensland on Sunday.
However, with Dragons back-rowers Ben Creagh and Beau Scott being kept in camp, the indications are that the 28-year-old is losing his battle.
Scott would replace the 2011 Clive Churchill Medallist in the run-on side, with Creagh, who has played in the front and back-row in the first two Origin clashes, coming off the bench.
It is the second year in succession Merrin has suffered the disappointment of being released for the decider in Brisbane.
He will now travel to Canberra with the Dragons for Monday's NRL clash with the Raiders, before joining up again with the Blues next Tuesday ahead of the game.