He hurt the joint during his side's 134-run defeat to Sri Lanka in the third and final Test at Trent Bridge, concluded with more than a day to spare, which saw the series end tied at 1-1.
Regular skipper Michael Vaughan (knee), fast bowlers Stephen Harmison (shin) and Simon Jones (knee) plus spinner Ashley Giles (hip/hernia), key members of the England side that beat Australia to reclaim the Ashes last year, all missed the whole of the Sri Lanka series.
Flintoff's injury could prevent him from taking part in the forthcoming five match One-day international campaign against Sri Lanka, which starts at Lord's on June 17.
The ankle problem meant the 28-year-old Lancashire all-rounder was unable to bowl at full speed during Sri Lanka's second innings at Trent Bridge.
"I struggled through this game -- on Friday I felt a little bit of soreness and in the second innings too," Flintoff said after Monday's defeat.
"I went for a scan yesterday (Sunday) which showed some bone fragments around the ankle.
"We'll have to see whether that's the cause of the inflammation around it.
"It is in the hands of the specialists and over the next 48 hours and towards the end of this week, we'll probably know more about it."
Muttiah Muralitharan took eight wickets, including all of England's top seven, to see Sri Lanka to a dramatic victory in Nottingham.
Flintoff scored one run in England's first innings and off-spin great Murali, whom he played alongside at Lancashire, had him out for a four-ball nought second time around.
The England skipper took three wickets for 52 runs as Sri Lanka scored 231 in their first innings but was far less effective when his side returned to the field again as the injury took its toll.
He claimed one for 38 in 13 overs but by the end of his bowling stint on Sunday, he was hobbling in at a much-reduced pace.
England, who take on Sri Lanka in a Twenty20 match at The Rose Bowl in Southampton on June 15, are due to name their one-day squad on Wednesday.
After the limited overs internationals, they face Pakistan in a four-Test series starting at Lord's on July 13.
Vaughan, who has begun his comeback by playing for Yorkshire this season, may feature in the Sri Lanka one-dayers.
But he admitted Saturday he was still some way short of full fitness, making the first Pakistan Test a more likely date for his international return.