Scarlett missed last week's massive win over Port Adelaide, as well as the loss to Fremantle in round three, with a sore back.
Thompson sounded doubtful about the 30-year-old's prospects of making a return against Carlton on Monday.
"He's still a little bit sore. I wouldn't say he's any certainty to play at this stage", Thompson said at Skilled Stadium on Tuesday morning.
"He'd have to improve a lot."
The Blues have fielded a shorter forward line this year after loss of spearhead Brendan Fevola, but Thompson said that would have no bearing on whether Scarlett was selected.
"They've got a small setup, which will be a challenge - it's rare to come up against a team that's hasn't got too many tall guys in the forward line, so our guys are going to have to really watch their dangerous small forwards.
"But Matty can play on a small bloke too, as [Andrew] Mackie can, Darren Milburn can; we don't mind Matty Scarlett playing on a small anytime."
The Fremantle game also saw the debut of Geelong's three-pronged tall forward line, with mature-age rookie James Podsiadly coming into the side to join Cameron Mooney and Tom Hawkins.
Podsiadly - who has now either tried out for, or been on the list of, five AFL clubs - has been a revelation, slipping in seamlessly to kick seven goals in his two matches.
Tellingly, half of his 22 marks have been contested.
Thompson said he would persist with the three-pronged attack for exactly as long as it kept working.
"[Those three players] were terrific on the weekend - they got a lot of ball supplied to them, which helped, but if it stands up we'll keep going with it.
"Podsy was just fantastic - played his second game of footy and ended up with five goals and marked the ball well.
"They didn't get in each other's way, so that was the most pleasing thing. If they can keep that up, they'll all be in the team."
Thompson said Hawkins, the youngest of the trio, should not feel under more pressure despite the presence of Podsiadly.
"Ultimately, Tom Hawkins is going to play a long time here, and so we're going to do whatever we can to make it happen, because we think he's got a huge upside and potential and he'll be a leader of the forward line for a long time.
"We won't be putting too much pressure on Tommy Hawkins."
