McManaman was the star of the Latics' FA Cup triumph last Saturday and was rewarded for his excellent form over the last few months of the season with a first call-up to Stuart Pearce's England squad for the tournament in Israel next month.
But the 22-year-old damaged ankle ligaments in Tuesday's 4-1 defeat by Arsenal, which condemned the Latics to relegation, and, although he will not need an operation, he is now in a race against time to be fit for the start of next season.
Martinez said: "It's good news because we expected the worst but good news means he's going to be out for the best part of three months, but he doesn't need surgery and that's really positive.
"But probably that puts him out of the Under-21s, which is a real shame because he really deserved to finish the season with that experience.
"Callum is disappointed but it's such a joy to see him playing his football. It's a joy for everyone. For me he's been one of the sparks of the season, and not just at Wigan.
"He's a real diamond of English football. He's got no reason to feel down at all."
McManaman has been replaced in the squad by Aston Villa's Nathan Delfouneso.
England squad for Under-21 European Championship:
Goalkeepers - Butland (Stoke), Steele (Middlesbrough), Rudd (Norwich)
Defenders - Caulker (Tottenham), Clyne (Southampton), Dawson (West Brom), Lees (Leeds), Rose (Sunderland, loan from Tottenham), Shaw (Southampton), Smith (Tottenham Hotspur), Wisdom (Liverpool)
Midfielders - Chalobah (Watford, loan from Chelsea), Henderson (Liverpool), Ince (Blackpool), Lansbury (Nottingham Forest), Lowe (Blackburn), McEachran (Chelsea), McManaman (Wigan Athletic), Shelvey (Liverpool), Townsend (QPR, loan from Tottenham)
Forwards - Zaha (Crystal Palace, loan from Manchester United), Marvin Sordell (Bolton), Connor Wickham (Sunderland), Nathan Delfouneso (Aston Villa)