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But he hopes his recovery effort inspires them to finish a sorry NRL season in a positive manner.
Scott is recovering in a Brisbane hospital after suffering a mild stroke on Sunday, with the forward missing the team's connecting flight following Saturday's heavy loss in Newcastle when he fell ill.
Doctors are confident he will make a full recovery and that the incident wasn't football related, the club said in a statement on Tuesday, however a return date to Townsville remains unknown.
Set to retire after this season, 34-year-old Scott has played 268 NRL games over 16 seasons as well as 22 State of Origin games for Queensland and 22 Tests for Australia.
With just three games to play, Green admitted it was unlikely Scott would add to that tally.
"Look, yeah it's pretty serious, I'd be surprised if he does play again," Green said.
"But I think that's the least of his worries at this stage.
"It's pretty upsetting news; everyone's just sort of processing it at the moment."
The Cowboys have limped through a disappointing campaign with just seven wins to sit 15th.
The coach said the playing group were "shocked" but expected a united response when they host Penrith on Friday.
"You can look at the legacies he's [Scott] left and use it as motivation to finish on a positive," he said.
"I'd be surprised if anyone didn't want to play ... if you look at what Matt's all about."
It is another blow for the club following serious injuries to Te Maire Martin (brain bleed) and Justin O'Neill (ruptured spleen) earlier this season.
Key players like Michael Morgan, Jason Taumalolo, Jordan McLean, Kyle Feldt and Scott have also missed chunks of the season through injury.
"I've never experienced in my time in rugby league ... so much at the one time," Green said of their injury toll.
"For it to be what it is [a stroke] is quite surprising and everyone's a little taken aback by what happened.
"All of your players, you build a pretty special relationship with them along the way."