El Duque, slated to be the No. 2 starter behind Tom Glavine in the Mets' shaky starting rotation, felt discomfort in his neck last season and the soreness returned this spring training, New York general manager Omar Minaya said before Thursday's workout.
Hernandez went 11-11 with a 4.66 ERA last season, including 9-7 with a 4.09 ERA after the Mets acquired him from Arizona in late May. The 41-year-old right-hander missed the playoffs because of a torn calf muscle.
New York already is without Pedro Martinez, out until midseason following rotator cuff surgery. Among those competing for starting jobs are prospects Philip Humber and Mike Pelfrey, and veterans Jorge Sosa, Chan Ho Park, Jason Vargas, Juan Padilla and Aaron Sele.