Watson was bowling the first ball of his sixth over against Western Australia at the WACA Ground when he pulled up sharply, clutching the back of his right leg.
Looking concerned, Watson conferred with Queensland captain Jimmy Maher and team-mates before leaving the ground with the team trainer.
Watson was considered a certain selection to bat at six against England in next week's first Test at the Gabba, allowing Australia to go with four fast bowlers and play wicketkeeper Adam Gilchrist at seven.
But if Watson is forced to withdraw Australia may look for a replacement all-rounder - possibly Andrew Symonds - pick five specialist bowlers, or another batsman.
The injury scare is the latest in a series of untimely set-backs for Watson, who has been restricted to three Tests since making his debut in January 2005.
After breaking into Australia's one-day team in 2002, stress fractures to his back at the start of 2003 forced him to miss the last World Cup.
Then last year he was drafted into the Test team with the intention of becoming the designated allrounder, but dislocated his shoulder while fielding in his second Test.