Watson has been troubled by a calf injury and tried this week to prove his fitness after missing the drawn series opener in Brisbane earlier this month.
But Clarke said doubts about Watson's injury prompted Australia go with an unchanged team for the second Test, which starts on Thursday.
"He has improved a lot over the last few days... but is probably a few days short of being 100 percent," Clarke said.
Rob Quiney, who made his Test debut in place of Watson in Brisbane, is expected to bat again at number three, while left-arm paceman Mitchell Starc remains the 12th man, Clarke said.
Australia: Michael Clarke (capt), David Warner, Ed Cowan, Rob Quiney, Ricky Ponting, Mike Hussey, Matthew Wade, Peter Siddle, James Pattinson, Nathan Lyon, Ben Hilfenhaus, Mitchell Starc (12th man).