Scarlett crashed down on the hard area in the centre of the MCG late in the Cats' nine-point win over Hawthorn on Easter Monday, and was helped from the ground holding his lower back.
The Cats face Fremantle on Sunday afternoon, and a trans-continental flight is not the best way to treat chronic back complaints.
Thompson admitted that he was concerned for his gun key defender.
"When his back goes, it really goes - I think it's pretty much seized at the moment," he said after the match.
"He landed pretty heavily on the hard part of the ground, so we'll have to wait and see how he pulls up.
"We play in six days, so it'll be a challenge."
The Cats also lost debutant Steven Motlop to a shoulder injury, and given he has already had two shoulder reconstructions, the club is anxiously waiting scans on the injury.
It was yet another tight win for the Cats over the Hawks, with last year's two wins both by single figures, and Thompson admitted he enjoyed beating the side that denied them the 2008 flag.
However, he said that match was never mentioned at Skilled Stadium.
"Yep, I must admit there is a real rivalry that we respect," he said.
"If you lose a grand final to a team, you never want that team to ever do that to you again - that's how I feel and I know the players feel like that.
"I know Hawthorn really enjoy playing us too... good matches."
Thompson said his side, which has won two of the last three flags, clearly still had the desire to keep winning.
"You just look at the result - if our hunger wasn't there and you get four goals down in a game then you wouldn't be able to play the way we did play in the last two quarters.
"Make no mistake, both sides, both teams, both clubs, would agree it was a pretty tough game of football.
"If we weren't prepared to play it that way we would have been beaten, I suppose."
While the 2008 decider is off-limits, CEO Brian Cook wasn't averse to mention the 2009 grand final when he speaking about the club's fourth win over the Hawks in their past five meetings.
"The grand final last year was probably the best game I've been involved with at the club, but this would have to go close to being second, I think, in terms of the way the boys have come back, it's fantastic," he told afl.com.au.
"i must admit, I was a little bit concerned at half-time, because I thought our boys might have run out of legs because of their (limited) pre-season, but when we got so close at three-quarter time, it was just 'we've got a chance'."
