The FA Cup finalists had feared the worst after the Honduras international was carried off on a stretcher during the draw with Tottenham in the Premier League last weekend.
The 30-year-old will now miss relegation-threatened Wigan's vital last four Premier League games as well as the cup final against Manchester City.
Martinez said: "We have had real negative news with Maynor Figueroa.
"He came off in the game really early and the scans have confirmed our worst fears.
"He is going to be out for the rest of the season and probably a longer period."
Figueroa has missed only two other games this season, one in the Capital One Cup and another, through suspension, in the Premier League.
The latest news has not made for a happy 30th birthday this week.
Martinez said: "He is Mr Reliable, someone who has never missed any sort of time during the time he has been at Wigan Athletic.
"Unfortunately he is now going to miss the most important period in a season."
- Sports & Recreation