The bowling all-rounder was named the team's all‑format captain in January, succeeding Alyssa Healy.
However, the 28-year-old has struggled with a back injury and was ruled out of the remainder of Australia's multi-format series against India during February and March.
Molineux captained Australia in the Twenty20 leg of their West Indies tour in March-April, but neither batted nor bowled in the first two matches and missed the other games.
The women's T20 World Cup begins on June 12 in England and Wales.
"We were clear from the start that the T20 World Cup was the priority series and we were going to make decisions around that," Flegler told reporters.
"The stress reaction in the back during the Indian series, not ideal, but things do happen. She's on track for the T20 World Cup and that's what the goal was at the start. It's probably a fair point to say it's unprecedented."