Hernandez will wear a protective boot for two weeks and then be re-evaluated, manager Willie Randolph said Wednesday.
El Duque is eligible to come off the disabled list Sunday, but won't be ready for a while. The Mets also are missing No. 2 starter Pedro Martinez, who strained his left hamstring in his first start of the season and is expected to miss four to six weeks.
In other injury news, second baseman Luis Castillo sat out Wednesday night's 8-2 over Philadelphia because of soreness in his surgically repaired right knee.
Castillo left Tuesday's home opener after the fourth inning and said he thought the cold weather probably contributed to the stiffness he felt in his knee. He received treatment Wednesday and said he felt better.
"I'm fine. A couple days, I'll be ready," he said. "I don't feel the pain like I did last year."
Damion Easley started at second base in place of Castillo.
"I think all year long he's been moving kind of gingerly anyway," Randolph said. "There's been times where he's kind of saved it a little bit, which means that he's not 100 percent.
"I would hope, assume that he's going to get stronger and better. Knees are different for different guys," the manager added.
Hernandez had toe surgery in the offseason and tried changing his signature, high-kick delivery during spring training to alleviate pressure from a bunion.
He went back to his familiar windup for a rehab start with Class-A St. Lucie last week, but still felt discomfort afterward and was scratched from his scheduled minor league outing this week.
"My hope is that once the two weeks are over, he's got to find a niche there somewhere that's going to be able to work for him," general manager Omar Minaya said.
The 42-year-old Hernandez had an MRI, and the Mets aren't sure when he might return. Randolph said it was too soon to know whether the right-hander could need more surgery.
"Usually when you put a boot on like that it's for rest," Randolph said. "We haven't really addressed surgery or anything like that."
The injuries to Martinez and Hernandez, two-fifths of New York's projected rotation, make Mike Pelfrey's performance especially important.
The right-hander made his first start of the year Wednesday night after compiling an 8.14 ERA in 21 innings during spring training. Pelfrey pitched five innings and gave up two runs on five hits while striking out three.
Selected ninth overall in the 2005 amateur draft, Pelfrey was 3-8 with a 5.57 ERA for the Mets last season. Now, he has a chance to secure a regular turn in the rotation for a while -- if he pitches well.
Asked if it was time for Pelfrey to establish himself in the majors, Randolph said: "This kid's got a lot of talent. It's been time. ... I think he's just about there. I believe in him. I think he's going to be a good major league pitcher."
Nelson Figueroa, pitching in the big leagues for the first time since 2004, is slated to start for the Mets on Friday night against Milwaukee.
Minaya said reliever Duaner Sanchez is close to returning. Sanchez has had two shoulder operations and hasn't pitched in the majors since getting hurt in a July 2006 taxi accident. He is slated to pitch on back-to-back days for Triple-A New Orleans on Friday and Saturday, a major step in his recovery.