Flintoff has been bowling at full pace for Lancashire
Andrew Flintoff will miss two of England's three Test matches against New Zealand because of a side strain.
The all-rounder experienced discomfort in the left side of his body during Lancashire's 232-run victory over Durham at Old Trafford on Friday.
Flintoff has been bowling at full pace after recovering from ankle surgery.
"It's frustrating to have picked up an injury at this time. I want nothing more than to return to the England side," said Flintoff.
He added: "I've put in a lot of hard work to get to this point after ankle surgery last year and I know I can overcome what isn't a significant injury....and will continue to do everything to make myself available for selection."
The England and Wales Cricket Board stressed Flintoff's side strain had no connection to his fourth ankle operation - which took place last October - and subsequent rehabilitation.
PAST FLINTOFF INJURIES
1999 Breaks foot while bowling in South Africa
2000 Leaves tour to Pakistan with a back injury
2002 Undergoes hernia operation - included in Ashes tour squad, but sent home with groin injury
2003 Misses Tests against Zimbabwe because of shoulder injury
2005 Suffers side strain in South Africa, then an ankle injury and is sent home for surgery
2006 Misses ODIs against Sri Lanka because of ankle problem - eventually has second operation
2007 Misses first two Tests against West Indies and has third ankle operation; plays in World Twenty20 but further surgery is performed in October
But it means Flintoff - who has not played a Test since the final Ashes match in Sydney in January 2007 - will not figure in the selection process until the third Test at Trent Bridge on 5 June at the earliest.
Lancashire chief executive Jim Cumbes said the timing of his latest injury was "unfortunate".
He told BBC Sport: "There doesn't appear to be any problems at all with his ankle, which is great news, but as often happens when you've been out for a while with an injury, you start to pick up other injuries.
"I think we've actually got it before it became a really bad strain...[but] it does mean he's going to be out for two to three weeks, probably.
"It is a shame for the lad because he was starting to get his confidence back, certainly with his bowling."
Even if he returns to fitness before the third Test against New Zealand starting on 5 June, it would be inconceivable for him to play without further first-team games for Lancashire.
That means he would probably also miss the one-day series against New Zealand, and set a fresh international comeback target of 10 July, the date of the first Test against South Africa.