Clarke's side go head-to-head with South Africa and hosts Zimbabwe over the coming two weeks as the nations begin their preparations for next year's World Cup.
Australia, the world's top-ranked one-day international team, meet Zimbabwe in the tournament opener in Harare on Monday, but may well be without their skipper after he left training early on Friday.
Cricket Australia confirmed the 33-year-old had experienced pain in his left leg and will be monitored over the coming days.
"We will monitor his condition closely over the next 24 hours to see how he [Clarke] responds to further treatment before making a decision on his management," team physiotherapist David Beakley said.
Should Clarke be deemed unfit, vice-captain George Bailey would lead Australia out in Harare.