Flintoff, 29, will bowl for Lancashire against Sussex at Hove in a county match from Wednesday. The amount of overs he bowls will depend on any pain felt in the ankle, Moores said.
"To be fair to Lancashire, they know their supporters want to watch Andrew play but they also know their responsibility to try and get him fit for England," Moores said.
Flintoff, England's only world-class all-rounder, has suffered intermittently for the last two years with a chronic ankle injury.
His latest setback came a fortnight ago and he had to miss the first two Tests against West Indies. The third starts on June 7.