Lancashire announced that he is being rested from the County's Cheltenham Gloucester Trophy quarterfinal against Yorkshire at Old Trafford on Wednesday as a precautionary measure.
County officials said: "Flintoff experienced pain in the posterior of his left ankle during the third Test match and underwent an X-Ray on Monday which was clear."
The all-rounder is a crucial component of the England Limited Overs side with his explosive batting and miserly pace bowling.
In his 71 One-day Internationals he has scored 1,599 runs at an average of 30.16 with a highest score of 84 and has taken 71 wickets at 25.08 with a career best of four for 14.
England open their One-day triangular NatWest Series campaign with a day-night match against New Zealand at Old Trafford on June 24.
The tournament also involves West Indies, with the final to be held at Lord's on July 10.